Mock Version: 1.2.17
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/epel-1-armhfp-751ee736e1cfff5746132e3ca9964d25adc8d69a/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=<mockbuild.trace_decorator.getLog object at 0xb6154a70>uid=995)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/R.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Wrote: /builddir/build/SRPMS/R-3.6.0-1.el7.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/epel-1-armhfp-751ee736e1cfff5746132e3ca9964d25adc8d69a/root'shell=Falseuid=995env={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0private_network=Truelogger=<mockbuild.trace_decorator.getLog object at 0xb6154a70>printOutput=False)
Executing command: ['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/R.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.mojojS
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf R-3.6.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/R-3.6.0.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd R-3.6.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):
+ echo 'Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/R-3.3.0-fix-java_path-in-javareconf.patch
+ /usr/bin/patch -p1 -b --suffix .fixpath --fuzz=0
patching file src/scripts/javareconf.in
Hunk #1 succeeded at 79 (offset 1 line).
+ cat
+ chmod +x /builddir/build/BUILD/R-3.6.0/R-prov
+ cat
+ chmod +x /builddir/build/BUILD/R-3.6.0/R-req
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.D3vCwz
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.6.0
+ echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library:/usr/share/R/library'\''}'
+ export R_RD4PDF=times,hyper
+ R_RD4PDF=times,hyper
+ sed -i 's|inconsolata,||g' etc/Renviron.in
+ export R_PDFVIEWER=/usr/bin/xdg-open
+ R_PDFVIEWER=/usr/bin/xdg-open
+ export R_PRINTCMD=lpr
+ R_PRINTCMD=lpr
+ export R_BROWSER=/usr/bin/xdg-open
+ R_BROWSER=/usr/bin/xdg-open
+ case "armv7hl" in
+ export CC=gcc
+ CC=gcc
+ export CXX=g++
+ CXX=g++
+ export F77=gfortran
+ F77=gfortran
+ export FC=gfortran
+ FC=gfortran
+ export 'FCFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard'
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard'
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro '
+ export LDFLAGS
+ '[' 1 == 1 ']'
+ '[' arm == ppc64le ']'
++ find . -name config.guess -o -name config.sub
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./tools/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./tools/config.sub
++ basename ./tools/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./tools/config.sub
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./tools/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./tools/config.guess
++ basename ./tools/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./tools/config.guess
+ ./configure --build=armv7hl-redhat-linux-gnu --host=armv7hl-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-system-tre --with-system-valgrind-headers --with-tcl-config=/usr/lib/tclConfig.sh --with-tk-config=/usr/lib/tkConfig.sh --enable-BLAS-shlib --enable-R-shlib --enable-prebuilt-html --enable-memory-profiling MAKEINFO=texi2any rdocdir=/usr/share/doc/R-3.6.0 rincludedir=/usr/include/R rsharedir=/usr/share/R
configure: WARNING: unrecognized options: --disable-dependency-tracking
./configure: line 27145: ::: command not found
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ cat CONFIGURE.log
+ grep -A30 'R is now' -
+ make V=1
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/m4'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/tools'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/html'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/html'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/etc'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/etc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/share'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/share'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include'
mkdir -p -- ../../include
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include/R_ext'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c blas.f -o blas.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
blas.f: In function 'drotmg':
blas.f:1614:0: warning: 'dh22' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH22=DH22*GAM
 ^
blas.f:1613:0: warning: 'dh21' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH21=DH21*GAM
 ^
blas.f:1591:0: warning: 'dh12' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH12=DH12*GAM
 ^
blas.f:1590:0: warning: 'dh11' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH11=DH11*GAM
 ^
blas.f: In function 'dspr':
blas.f:2409:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
blas.f: In function 'dspr2':
blas.f:2618:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY
 ^
blas.f:2618:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:2618:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:2618:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f: In function 'dsyr':
blas.f:3451:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
blas.f: In function 'dsyr2':
blas.f:3659:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, KX, KY
 ^
blas.f:3659:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:3659:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:3659:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f: In function 'dtbmv':
blas.f:4550:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
blas.f: In function 'dtbsv':
blas.f:4896:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
blas.f: In function 'dtpmv':
blas.f:5198:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
blas.f: In function 'dtpsv':
blas.f:5500:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
blas.f: In function 'dtrmv':
blas.f:6157:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
blas.f: In function 'dtrsv':
blas.f:6824:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c cmplxblas.f -o cmplxblas.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
cmplxblas.f:4796.26:
                  RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J )         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplxblas.f:4808.26:
                  RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J )         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplxblas.f: In function 'zher2':
cmplxblas.f:1130:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, KX, KY
 ^
cmplxblas.f:1130:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:1130:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:1130:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f: In function 'ztrmv':
cmplxblas.f:2208:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'ztrsv':
cmplxblas.f:2946:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'zher':
cmplxblas.f:4386:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'zhpr':
cmplxblas.f:5195:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
cmplxblas.f: In function 'zhpr2':
cmplxblas.f:5423:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY
 ^
cmplxblas.f:5423:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:5423:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:5423:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f: In function 'ztbmv':
cmplxblas.f:6649:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
cmplxblas.f: In function 'ztbsv':
cmplxblas.f:7030:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
cmplxblas.f: In function 'ztpmv':
cmplxblas.f:7367:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
cmplxblas.f: In function 'ztpsv':
cmplxblas.f:7708:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libRblas.so blas.o  cmplxblas.o -lgfortran -lm
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
mkdir -p -- /builddir/build/BUILD/R-3.6.0/lib
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/appl'
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/appl'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c integrate.c -o integrate.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c interv.c -o interv.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c maxcol.c -o maxcol.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c optim.c -o optim.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pretty.c -o pretty.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c uncmin.c -o uncmin.o
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dchdc.f -o dchdc.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dpbfa.f -o dpbfa.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dpbsl.f -o dpbsl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dpoco.f -o dpoco.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dpodi.f -o dpodi.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dpofa.f -o dpofa.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dposl.f -o dposl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dqrdc.f -o dqrdc.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dqrdc2.f -o dqrdc2.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dqrls.f -o dqrls.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dqrsl.f -o dqrsl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dqrutl.f -o dqrutl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dsvdc.f -o dsvdc.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dtrco.f -o dtrco.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dtrsl.f -o dtrsl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o 
ranlib libappl.a
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/appl'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mlutils.c -o mlutils.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c d1mach.c -o d1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c i1mach.c -o i1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmax2.c -o fmax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmin2.c -o fmin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fprec.c -o fprec.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fround.c -o fround.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ftrunc.c -o ftrunc.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sign.c -o sign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fsign.c -o fsign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imax2.c -o imax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imin2.c -o imin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chebyshev.c -o chebyshev.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c log1p.c -o log1p.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgammacor.c -o lgammacor.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gammalims.c -o gammalims.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stirlerr.c -o stirlerr.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bd0.c -o bd0.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma.c -o gamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgamma.c -o lgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c beta.c -o beta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lbeta.c -o lbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c polygamma.c -o polygamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cospi.c -o cospi.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_i.c -o bessel_i.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_j.c -o bessel_j.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_k.c -o bessel_k.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_y.c -o bessel_y.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c choose.c -o choose.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c snorm.c -o snorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sexp.c -o sexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgamma.c -o dgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgamma.c -o pgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgamma.c -o qgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgamma.c -o rgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbeta.c -o dbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbeta.c -o pbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbeta.c -o qbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbeta.c -o rbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dunif.c -o dunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c punif.c -o punif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qunif.c -o qunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c runif.c -o runif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnorm.c -o dnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnorm.c -o pnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnorm.c -o rnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlnorm.c -o dlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plnorm.c -o plnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlnorm.c -o qlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlnorm.c -o rlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c df.c -o df.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pf.c -o pf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qf.c -o qf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rf.c -o rf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnf.c -o dnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dt.c -o dt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pt.c -o pt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qt.c -o qt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rt.c -o rt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnt.c -o dnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dchisq.c -o dchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pchisq.c -o pchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qchisq.c -o qchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rchisq.c -o rchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnchisq.c -o rnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbinom.c -o dbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbinom.c -o pbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbinom.c -o qbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbinom.c -o rbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rmultinom.c -o rmultinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dcauchy.c -o dcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pcauchy.c -o pcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qcauchy.c -o qcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rcauchy.c -o rcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dexp.c -o dexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pexp.c -o pexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qexp.c -o qexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rexp.c -o rexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgeom.c -o dgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgeom.c -o pgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgeom.c -o qgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgeom.c -o rgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dhyper.c -o dhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c phyper.c -o phyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qhyper.c -o qhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rhyper.c -o rhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbinom.c -o dnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbinom.c -o pnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbinom.c -o qnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnbinom.c -o rnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dpois.c -o dpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ppois.c -o ppois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qpois.c -o qpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpois.c -o rpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dweibull.c -o dweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pweibull.c -o pweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qweibull.c -o qweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rweibull.c -o rweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlogis.c -o dlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plogis.c -o plogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlogis.c -o qlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlogis.c -o rlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnchisq.c -o dnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnchisq.c -o pnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnchisq.c -o qnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbeta.c -o dnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbeta.c -o pnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbeta.c -o qnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnf.c -o pnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnt.c -o pnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnf.c -o qnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnt.c -o qnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ptukey.c -o ptukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qtukey.c -o qtukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c toms708.c -o toms708.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c wilcox.c -o wilcox.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/unix'
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rembedded.c -o Rembedded.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dynload.c -o dynload.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c system.c -o system.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sys-unix.c -o sys-unix.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sys-std.c -o sys-std.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c X11.c -o X11.o
ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/unix'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -Wl,-z,relro  -DR_HOME='"/builddir/build/BUILD/R-3.6.0"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/unix'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making altclasses.d from altclasses.c
making altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c CommandLineArgs.c -o CommandLineArgs.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rdynload.c -o Rdynload.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Renviron.c -o Renviron.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c RNG.c -o RNG.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agrep.c -o agrep.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c altclasses.c -o altclasses.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c altrep.c -o altrep.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c apply.c -o apply.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c arithmetic.c -o arithmetic.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c array.c -o array.o
array.c: In function 'mayHaveNaNOrInf_simd':
array.c:654:0: warning: ignoring #pragma omp simd [-Wunknown-pragmas]
     #pragma omp simd reduction(+:s)
 ^
array.c: In function 'cmayHaveNaNOrInf_simd':
array.c:680:0: warning: ignoring #pragma omp simd [-Wunknown-pragmas]
     #pragma omp simd reduction(+:s)
 ^
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c attrib.c -o attrib.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bind.c -o bind.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c builtin.c -o builtin.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c character.c -o character.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coerce.c -o coerce.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c colors.c -o colors.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c complex.c -o complex.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c connections.c -o connections.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c context.c -o context.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cum.c -o cum.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dcf.c -o dcf.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c datetime.c -o datetime.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c debug.c -o debug.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c deparse.c -o deparse.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devices.c -o devices.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dotcode.c -o dotcode.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dounzip.c -o dounzip.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dstruct.c -o dstruct.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c duplicate.c -o duplicate.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c edit.c -o edit.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c engine.c -o engine.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c envir.c -o envir.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c errors.c -o errors.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c eval.c -o eval.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c format.c -o format.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gevents.c -o gevents.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gram.c -o gram.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gram-ex.c -o gram-ex.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c graphics.c -o graphics.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c grep.c -o grep.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c identical.c -o identical.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c inlined.c -o inlined.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c inspect.c -o inspect.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c internet.c -o internet.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c iosupport.c -o iosupport.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lapack.c -o lapack.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c list.c -o list.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c localecharset.c -o localecharset.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c logic.c -o logic.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c main.c -o main.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mapply.c -o mapply.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c match.c -o match.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c memory.c -o memory.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c names.c -o names.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c objects.c -o objects.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c options.c -o options.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c paste.c -o paste.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c platform.c -o platform.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plot.c -o plot.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plot3d.c -o plot3d.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plotmath.c -o plotmath.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c print.c -o print.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c printarray.c -o printarray.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c printvector.c -o printvector.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c printutils.c -o printutils.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qsort.c -o qsort.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c radixsort.c -o radixsort.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c random.c -o random.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c raw.c -o raw.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c registration.c -o registration.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c relop.c -o relop.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlocale.c -o rlocale.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c saveload.c -o saveload.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c scan.c -o scan.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c seq.c -o seq.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c serialize.c -o serialize.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sort.c -o sort.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c source.c -o source.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c split.c -o split.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sprintf.c -o sprintf.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c startup.c -o startup.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c subassign.c -o subassign.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c subscript.c -o subscript.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c subset.c -o subset.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c summary.c -o summary.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sysutils.c -o sysutils.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c times.c -o times.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c unique.c -o unique.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c util.c -o util.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c version.c -o version.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c g_alab_her.c -o g_alab_her.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c g_cntrlify.c -o g_cntrlify.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c g_fontdb.c -o g_fontdb.o
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c g_her_glyph.c -o g_her_glyph.o
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c xxxpr.f -o xxxpr.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro   -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o`     -L"../../lib" -lRblas -lgfortran -lm   -lreadline  -ltre -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
mkdir -p -- /builddir/build/BUILD/R-3.6.0/bin/exec
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
gcc -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rmain.c -o Rmain.o
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L"../../lib" -Wl,-z,relro  -o R.bin Rmain.o  -lR -lRblas
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
making Rhttpd.d from Rhttpd.c
making Rsock.d from Rsock.c
making internet.d from internet.c
making libcurl.d from libcurl.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sock.d from sock.c
making sockconn.d from sockconn.c
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c Rsock.c -o Rsock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c internet.c -o internet.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c libcurl.c -o libcurl.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c nanoftp.c -o nanoftp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c nanohttp.c -o nanohttp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c sock.c -o sock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard   -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl   -lR  
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILD/R-3.6.0/modules
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
making Lapack.d from Lapack.c
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
gfortran -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules -c dlamch.f -o dlamch.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dlapack.f -o dlapack.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
SRC/iparam2stage.F:6871.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:6885.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:9161.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:9776.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16788.28:
               LWORK_DGEQRF=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16792.28:
               LWORK_DORMQR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16807.28:
               LWORK_DGEBRD=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16811.28:
               LWORK_DORMBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:98487.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16815.28:
               LWORK_DORGBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16839.31:
                  LWORK_DGELQF=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16843.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16847.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16851.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16855.31:
                  LWORK_DORMLQ=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16875.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16879.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16883.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36428.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:35370.13:
      LOPT = WORK( M+NP+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36726.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36074.13:
      LOPT = WORK( P+MN+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:124156.14:
      LWMIN = MAX( DBLE( LWMIN ), DBLE( WORK( 1 ) ) )                   
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:124157.15:
      LIWMIN = MAX( DBLE( LIWMIN ), DBLE( IWORK( 1 ) ) )                
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:136875.13:
      LOPT = MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) )                     
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:136876.14:
      LIOPT = MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) )                  
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:138054.21:
            LWKOPT = WORK(1)                                            
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:77843.34:
      SUBROUTINE DLARRV( N, VL, VU, D, L, PIVMIN,                       
                                  1
Warning: Unused dummy argument 'vu' at (1)
SRC/iparam2stage.F:74326.54:
      SUBROUTINE DLARRC( JOBT, N, VL, VU, D, E, PIVMIN,                 
                                                      1
Warning: Unused dummy argument 'pivmin' at (1)
SRC/iparam2stage.F:46267.45:
     $                   RELTOL, PIVMIN, D, E, E2, NVAL, AB, C, MOUT,   
                                             1
Warning: Unused dummy argument 'e' at (1)
SRC/iparam2stage.F:58693.55:
      INTEGER FUNCTION DLANEG( N, D, LLD, SIGMA, PIVMIN, R )            
                                                       1
Warning: Unused dummy argument 'pivmin' at (1)
SRC/iparam2stage.F:612.68:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                                    1
Warning: Unused dummy argument 'lwork' at (1)
SRC/iparam2stage.F:612.51:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                   1
Warning: Unused dummy argument 'n' at (1)
SRC/iparam2stage.F:612.48:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                1
Warning: Unused dummy argument 'opts' at (1)
SRC/iparam2stage.F:128949.23:
     $           ABSTOL, M, W, Z, LDZ, ISUPPZ, WORK, LWORK, IWORK,      
                       1
Warning: Unused dummy argument 'abstol' at (1)
dlapack.f: In function 'dlatrs':
dlapack.f:95122:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dlatps':
dlapack.f:93997:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dlatbs':
dlapack.f:92881:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dsptrf':
dlapack.f:126563:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dtptri':
dlapack.f:155012:0: warning: 'jclast' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                     AP( JCLAST ), AP( JC+1 ), 1 )
 ^
dlapack.f: In function 'dlaruv':
dlapack.f:79873:0: warning: 'it4' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 4 ) = IT4
 ^
dlapack.f:79872:0: warning: 'it3' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 3 ) = IT3
 ^
dlapack.f:79871:0: warning: 'it2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 2 ) = IT2
 ^
dlapack.f:79870:0: warning: 'it1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 1 ) = IT1
 ^
dlapack.f: In function 'dstein':
dlapack.f:129376:0: warning: 'xjm' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ABS( XJ-XJM ).GT.ORTOL )
 ^
dlapack.f:129376:0: warning: 'ortol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:129362:0: warning: 'onenrm' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $            ABS( WORK( INDRV1+JMAX ) )
 ^
dlapack.f:129396:0: warning: 'dtpcrt' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( NRM.LT.DTPCRT )
 ^
dlapack.f: In function 'dlaed6':
dlapack.f:49708:0: warning: 'sclinv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $   TAU = TAU*SCLINV
 ^
dlapack.f: In function 'dgghrd':
dlapack.f:35771:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
dlapack.f: In function 'dgetc2':
dlapack.f:30048:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          A( N, N ) = SMIN
 ^
dlapack.f:30030:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $      CALL DSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 )
 ^
dlapack.f:29960:0: warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IP, IPV, J, JP, JPV
 ^
dlapack.f: In function 'dlasy2':
dlapack.f:91209:0: warning: 'jpsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( JPSV.NE.I )
 ^
dlapack.f:91203:0: warning: 'ipsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IPSV.NE.I ) THEN
 ^
dlapack.f: In function 'dtgevc':
dlapack.f:147008:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILBACK ) THEN
 ^
dlapack.f: In function 'dlasq4':
dlapack.f:88702:0: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       TAU = S
 ^
dlapack.f: In function 'dsytf2':
dlapack.f:139620:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dlals0':
dlapack.f:57295:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
dlapack.f: In function 'dlasd8':
dlapack.f:85755:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   / ( DSIGMA( I )+DJ )
 ^
dlapack.f: In function 'dlantr':
dlapack.f:62441:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantp':
dlapack.f:62069:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantb':
dlapack.f:61724:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansy':
dlapack.f:61464:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlanst':
dlapack.f:61256:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM
 ^
dlapack.f: In function 'dlansp':
dlapack.f:61009:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansb':
dlapack.f:59803:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlapy2':
dlapack.f:63553:0: warning: '__result_dlapy2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION FUNCTION DLAPY2( X, Y )
 ^
dlapack.f: In function 'dlahr2':
dlapack.f:55512:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
dlapack.f: In function 'dlaed8':
dlapack.f:50392:0: warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2
 ^
dlapack.f: In function 'dlaed2':
dlapack.f:47548:0: warning: 'pj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   N2, NJ, PJ
 ^
dlapack.f: In function 'dlahqr':
dlapack.f:55126:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DO 100 J = K, I2
 ^
dlapack.f: In function 'dlasd7':
dlapack.f:85161:0: warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M, N,
 ^
dlapack.f: In function 'dlasd2':
dlapack.f:82313:0: warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            CT, I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M,
 ^
dlapack.f: In function 'dlarrf':
dlapack.f:76623:0: warning: 'indx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF(INDX.EQ.1) THEN
 ^
dlapack.f: In function 'dlanhs':
dlapack.f:59577:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dhgeqz':
dlapack.f:43147:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ ) THEN
 ^
dlapack.f:42638:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
dlapack.f:42861:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( .NOT.ILSCHR ) THEN
 ^
dlapack.f: In function 'dlangt':
dlapack.f:59367:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM, TEMP
 ^
dlapack.f: In function 'dlange':
dlapack.f:59164:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
dlapack.f: In function 'dtrsen':
dlapack.f:159919:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WORK( 1 ) = LWMIN
 ^
dlapack.f:159920:0: warning: 'liwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IWORK( 1 ) = LIWMIN
 ^
dlapack.f: In function 'dlangb':
dlapack.f:58950:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
SRC/iparam2stage.F: In function 'iparmq':
SRC/iparam2stage.F:770:0: warning: 'ns' may be used uninitialized in this function [-Wmaybe-uninitialized]
SRC/iparam2stage.F:761:0: warning: 'nh' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dlaed0':
dlapack.f:46983:0: warning: 'iwrem' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      IWORK( SUBPBS+1 ), INFO )
 ^
dlapack.f:46983:0: warning: 'iqptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iq' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iprmpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iperm' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'igivpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'igivcl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormql':
dlapack.f:102784:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
dlapack.f: In function 'dorgql':
dlapack.f:99539:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dsyevx':
dlapack.f:135615:0: warning: 'lwkopt' may be used uninitialized in this function [-Wmaybe-uninitialized]
       WORK( 1 ) = LWKOPT
 ^
dlapack.f: In function 'dlarrd':
dlapack.f:75191:0: warning: 'wul' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( W( JE ).GE.WUL .AND. IDISCU.GT.0 ) THEN
 ^
dlapack.f:75174:0: warning: 'wlu' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( W( JE ).LE.WLU .AND. IDISCL.GT.0 ) THEN
 ^
dlapack.f: In function 'dlarre':
dlapack.f:75712:0: warning: 'irange' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $       ((IRANGE.EQ.VALRNG).AND.(D(1).GT.VL).AND.(D(1).LE.VU)).OR.
 ^
dlapack.f:76205:0: warning: 'wend' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WBEGIN = WEND + 1
 ^
dlapack.f:76191:0: warning: 'mb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             DO 165 I = M - MB + 1, M
 ^
dlapack.f: In function 'dormrq':
dlapack.f:104041:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
dlapack.f: In function 'dtgsyl':
dlapack.f:152216:0: warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCALE = SCALE2
 ^
dlapack.f: In function 'dtgsna':
dlapack.f:150520:0: warning: 'cond' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           COND )
 ^
dlapack.f: In function 'dbdsdc':
dlapack.f:1544:0: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      WORK( WSTART ), IWORK, INFO )
 ^
dlapack.f:1544:0: warning: 'poles' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'ivt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'is' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'ic' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'givnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'givcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'difr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'difl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormrz':
dlapack.f:104412:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( LWORK.LT.NW*NB+TSIZE ) THEN
 ^
dlapack.f: In function 'dtzrzf':
dlapack.f:163493:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dgehrd':
dlapack.f:13098:0: warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized]
          DO 40 I = ILO, IHI - 1 - NX, NB
 ^
dlapack.f: In function 'dgbsvx':
dlapack.f:5390:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:5405:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f: In function 'dgeesx':
dlapack.f:9704:0: warning: 'maxwrk' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   MAXWRK, MINWRK
 ^
dlapack.f: In function 'dgelss':
dlapack.f:16972:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f: In function 'dgesvd':
dlapack.f:24782:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f:24342:0: warning: 'bdspac' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            BDSPAC, BLK, CHUNK, I, IE, IERR, IR, ISCL,
 ^
dlapack.f:27577:0: warning: 'ie' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IE.LT.2 ) THEN
 ^
dlapack.f:24345:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
dlapack.f: In function 'dgesvx':
dlapack.f:29665:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:29680:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f: In function 'dlahrd':
dlapack.f:55813:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
dlapack.f: In function 'dlansf':
dlapack.f:60141:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, S, VALUE, AA, TEMP
 ^
dlapack.f: In function 'dorcsd':
dlapack.f:97738:0: warning: 'itauq2' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:97738:0: warning: 'itauq1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97738:0: warning: 'itaup2' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97738:0: warning: 'itaup1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97802:0: warning: 'iorgqr' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGQR), LORGQRWORK, INFO )
 ^
dlapack.f:97784:0: warning: 'iorglq' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGLQ), LORGLQWORK, INFO )
 ^
dlapack.f:97738:0: warning: 'iorbdb' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:97812:0: warning: 'ibbcsd' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IB22E), WORK(IBBCSD), LBBCSDWORK, INFO )
 ^
dlapack.f:97812:0: warning: 'ib22e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib22d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib21e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib21d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib12e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib12d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib11e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib11d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dorgrq':
dlapack.f:100327:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dpbsvx':
dlapack.f:106741:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:106741:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dposvx':
dlapack.f:110628:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:110628:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dppsvx':
dlapack.f:113309:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:113309:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c cmplx.f -o cmplx.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
cmplx.f:1780.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
cmplx.f:1794.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
cmplx.f:2456.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2475.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2500.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2519.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21690.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21730.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21774.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21808.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:3759.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:50903.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:18862.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:38115.26:
               E( I-1 ) = ALPHA                                         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:38169.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19996.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19582.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19610.23:
            D( I+1 ) = A( I+1, I+1 )                                    
                       1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19613.18:
         D( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19626.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19655.21:
            D( I ) = A( I, I )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19658.18:
         D( N ) = A( N, N )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:20028.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19253.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39333.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39352.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39774.18:
            AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( 1, J ), 1,         
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39801.18:
            AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( J, 1 ), LDA,       
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f: In function 'zsyr':
cmplx.f:42206:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplx.f: In function 'zsytf2':
cmplx.f:42910:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
cmplx.f: In function 'zlaed8':
cmplx.f:23865:0: warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2
 ^
cmplx.f: In function 'zlantr':
cmplx.f:28016:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zlanhe':
cmplx.f:27532:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
cmplx.f: In function 'ztgevc':
cmplx.f:44370:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( ILBACK ) THEN
 ^
cmplx.f:44246:0: warning: 'ilall' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILALL ) THEN
 ^
cmplx.f: In function 'zlange':
cmplx.f:27310:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
cmplx.f: In function 'zgetc2':
cmplx.f:14939:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   BIGNUM, EPS, SMIN, SMLNUM, XMAX
 ^
cmplx.f:15008:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $      CALL ZSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 )
 ^
cmplx.f:14938:0: warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IP, IPV, J, JP, JPV
 ^
cmplx.f: In function 'zgghrd':
cmplx.f:18613:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
cmplx.f: In function 'zlanhs':
cmplx.f:27775:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zhgeqz':
cmplx.f:20898:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ )
 ^
cmplx.f:20840:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
cmplx.f:20746:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( .NOT.ILSCHR ) THEN
 ^
cmplx.f: In function 'zlals0':
cmplx.f:25696:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                            DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
cmplx.f: In function 'zlahqr':
cmplx.f:24616:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                      IF( I2.GT.J )
 ^
cmplx.f: In function 'zlahr2':
cmplx.f:24973:0: warning: 'IMAGPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
cmplx.f:24872:0: warning: 'REALPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       COMPLEX*16        EI
 ^
cmplx.f: In function 'ztgsyl':
cmplx.f:46945:0: warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCALE = SCALE2
 ^
cmplx.f: In function 'ztrsen':
cmplx.f:49023:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ELSE IF( LWORK.LT.LWMIN .AND. .NOT.LQUERY ) THEN
 ^
cmplx.f: In function 'zunmql':
cmplx.f:55231:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
cmplx.f: In function 'zungql':
cmplx.f:51959:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
cmplx.f: In function 'zgehrd':
cmplx.f:4925:0: warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized]
          DO 40 I = ILO, IHI - 1 - NX, NB
 ^
cmplx.f: In function 'zgelsd':
cmplx.f:6411:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f: In function 'zgesvd':
cmplx.f:11158:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f:10741:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
cmplx.f: In function 'zgesvx':
cmplx.f:14642:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
cmplx.f:14657:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
cmplx.f: In function 'zungrq':
cmplx.f:52750:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libRlapack.so dlamch.o dlapack.o cmplx.o   -L"../../../lib" -lRblas -lgfortran -lm 
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Lapack.c -o Lapack.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o lapack.so  Lapack.o  -lR  -L"../../../lib" -lRlapack -L"../../../lib" -lRblas -lgfortran -lm
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
/builddir/build/BUILD/R-3.6.0/lib/libRlapack.so is unchanged
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
making devX11.d from devX11.c
making rotated.d from rotated.c
making rbitmap.d from rbitmap.c
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
gcc -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/fribidi -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/pixman-1 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devX11.c -o devX11.o
gcc -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/fribidi -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/pixman-1 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rotated.c -o rotated.o
gcc -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/fribidi -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/pixman-1 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbitmap.c -o rbitmap.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff   -ljpeg   -lpng15   -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -lR -lm 
gcc -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/fribidi -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/pixman-1 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dataentry.c -o dataentry.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -lR -lm 
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
mkdir -p -- ../../library
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/profile'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/translations'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/translations'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/translations'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
building package 'base'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c text.c -o text.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rmd5.c -o Rmd5.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c md5.c -o md5.o
md5.c: In function 'md5_finish_ctx':
md5.c:102:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad] = SWAP (ctx->total[0] << 3);
   ^
md5.c:103:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad + 4] = SWAP ((ctx->total[1] << 3) |
   ^
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c signals.c -o signals.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c install.c -o install.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c getfmts.c -o getfmts.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c http.c -o http.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gramLatex.c -o gramLatex.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gramRd.c -o gramRd.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/compiler'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c io.c -o io.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c size.c -o size.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sock.c -o sock.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stubs.c -o stubs.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/utils'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c axis_scales.c -o axis_scales.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chull.c -o chull.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devices.c -o devices.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stubs.c -o stubs.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c colors.c -o colors.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devCairo.c -o devCairo.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devPicTeX.c -o devPicTeX.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devPS.c -o devPS.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c devQuartz.c -o devQuartz.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
make[9]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/fribidi -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/pixman-1 -I/usr/include/libdrm -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cairoBM.c -o cairoBM.o
gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro  -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff   -ljpeg   -lpng15   -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo   -L"../../../../../lib" -lR -lm 
make[9]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
make[8]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
make[7]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo'
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grDevices'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c base.c -o base.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c graphics.c -o graphics.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c par.c -o par.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plot.c -o plot.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plot3d.c -o plot3d.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stem.c -o stem.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/graphics'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c kmeans.c -o kmeans.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ansari.c -o ansari.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bandwidths.c -o bandwidths.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chisqsim.c -o chisqsim.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c d2x2xk.c -o d2x2xk.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fexact.c -o fexact.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c kendall.c -o kendall.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ks.c -o ks.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c line.c -o line.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c smooth.c -o smooth.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c prho.c -o prho.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c swilk.c -o swilk.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ksmooth.c -o ksmooth.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c loessc.c -o loessc.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c monoSpl.c -o monoSpl.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c isoreg.c -o isoreg.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Srunmed.c -o Srunmed.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dblcen.c -o dblcen.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c distance.c -o distance.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c hclust-utils.c -o hclust-utils.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nls.c -o nls.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rWishart.c -o rWishart.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c HoltWinters.c -o HoltWinters.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c PPsum.c -o PPsum.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c arima.c -o arima.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c burg.c -o burg.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c filter.c -o filter.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mAR.c -o mAR.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pacf.c -o pacf.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c starma.c -o starma.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c port.c -o port.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c family.c -o family.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sbart.c -o sbart.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c approx.c -o approx.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c loglin.c -o loglin.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lowess.c -o lowess.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c massdist.c -o massdist.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c splines.c -o splines.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lm.c -o lm.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c complete_cases.c -o complete_cases.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cov.c -o cov.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c deriv.c -o deriv.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fft.c -o fft.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fourier.c -o fourier.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c model.c -o model.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c optim.c -o optim.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c optimize.c -o optimize.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c integrate.c -o integrate.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c random.c -o random.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c distn.c -o distn.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c zeroin.c -o zeroin.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rcont.c -o rcont.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c influence.c -o influence.o
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c bsplvd.f -o bsplvd.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c bvalue.f -o bvalue.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c bvalus.f -o bvalus.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c loessf.f -o loessf.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
loessf.f:59.14:
            j=DBLE(j)/2.D0                                              
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1893.14:
            m=DBLE(l+u)/2.D0                                            
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1398.20:
                  i=phi(pi(ii))                                         
                    1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:927.12:
         lg=DBLE(lg)/2.D0                                               
            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:522.22:
      if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0                            
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1204.13:
      ifloor=x                                                          
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:834.22:
      if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0                            
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1582.18:
               i1=dble((d+2)*(d+1))/2.d0                                
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:472.25:
      subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                         1
Warning: Unused dummy argument 'n' at (1)
loessf.f:472.39:
      subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                                       1
Warning: Unused dummy argument 'nc' at (1)
loessf.f:827.31:
      subroutine ehg197(deg,tau,d,f,dk,trl)                             
                               1
Warning: Unused dummy argument 'tau' at (1)
loessf.f:1984.31:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                               1
Warning: Unused dummy argument 'kappa' at (1)
loessf.f:1984.47:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                                               1
Warning: Unused dummy argument 'nv' at (1)
loessf.f:1984.53:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                                                     1
Warning: Unused dummy argument 'nvmax' at (1)
loessf.f:1497.50:
      subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)               
                                                  1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1497.53:
      subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)               
                                                     1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1648.30:
      subroutine lowese(iv,liv,lv,wv,m,z,s)                             
                              1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1648.33:
      subroutine lowese(iv,liv,lv,wv,m,z,s)                             
                                 1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1667.39:
      subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)             
                                       1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1667.42:
      subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)             
                                          1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1699.30:
      subroutine lowesl(iv,liv,lv,wv,m,z,l)                             
                              1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1699.33:
      subroutine lowesl(iv,liv,lv,wv,m,z,l)                             
                                 1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1721.33:
      subroutine lowesr(yy,iv,liv,lv,wv)                                
                                 1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1721.36:
      subroutine lowesr(yy,iv,liv,lv,wv)                                
                                    1
Warning: Unused dummy argument 'lv' at (1)
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c ppr.f -o ppr.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c qsbart.f -o qsbart.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c sgram.f -o sgram.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c sinerp.f -o sinerp.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c sslvrg.f -o sslvrg.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c stxwx.f -o stxwx.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c hclust.f -o hclust.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c kmns.f -o kmns.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c eureka.f -o eureka.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c stl.f -o stl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules -c portsrc.f -o portsrc.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
portsrc.f: In function 'i7do':
portsrc.f:6658:0: warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
          NCOMP = NCOMP + 1
 ^
portsrc.f:6678:0: warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
          JPU = JPNTR(JCOL+1) - 1
 ^
portsrc.f: In function 'df7dhb':
portsrc.f:12614:0: warning: 'pp1o2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       HPI = HES + PP1O2
 ^
portsrc.f: In function 'dl7mst':
portsrc.f:5516:0: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
portsrc.f:5653:0: warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
               IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
 ^
portsrc.f: In function 'dg7qts':
portsrc.f:10407:0: warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
 ^
portsrc.f:10324:0: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
portsrc.f:10319:0: warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
       LK = DMAX1(LK, PHI*W(PHIPIN))
 ^
portsrc.f:10461:0: warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (KA .GE. KAMIN) GO TO 340
 ^
portsrc.f: In function 'dd7dgb':
portsrc.f:12238:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:12241:0: warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(DST0) = DNWTST
 ^
portsrc.f: In function 'dg7qsb':
portsrc.f:2510:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:2509:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  60   V(DST0) = DS0
 ^
portsrc.f: In function 'dl7msb':
portsrc.f:8169:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:8168:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  90   V(DST0) = DS0
 ^
portsrc.f: In function 'df7hes':
portsrc.f:8647:0: warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
  210  IV(FDH) = HES
 ^
portsrc.f: In function 'dparck':
portsrc.f:3582:0: warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (LIV .LT. MIV2) GO TO 300
 ^
portsrc.f: In function 'drn2gb':
portsrc.f:12074:0: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  270  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
portsrc.f:12031:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:12031:0: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f: In function 'drn2g':
portsrc.f:453:0: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  300  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
portsrc.f:361:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:361:0: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c lminfl.f -o lminfl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -L../../../../lib -lRlapack -L../../../../lib -lRblas -lgfortran -lm -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/datasets'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/datasets'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
making utils.d from utils.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c do_substitute_direct.c -o do_substitute_direct.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c methods_list_dispatch.c -o methods_list_dispatch.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c slot.c -o slot.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c class_support.c -o class_support.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c tests.c -o tests.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/methods'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid/src'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gpar.c -o gpar.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c grid.c -o grid.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c just.c -o just.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c layout.c -o layout.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c matrix.c -o matrix.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c register.c -o register.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c state.c -o state.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c unit.c -o unit.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c util.c -o util.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c viewport.c -o viewport.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/grid'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines/src'
making splines.d from splines.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c splines.c -o splines.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
byte-compiling package 'splines'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/splines'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
byte-compiling package 'stats4'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/stats4'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src'
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c tcltk.c -o tcltk.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c tcltk_unix.c -o tcltk_unix.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib -ltcl8.5 -L/usr/lib -ltk8.5 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
byte-compiling package 'tcltk'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/tcltk'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
make[5]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel/src'
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rngstream.c -o rngstream.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fork.c -o fork.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
make[4]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
byte-compiling package 'parallel'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/parallel'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/base'
installing parsed NAMESPACE files
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/tests'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/tests'
you should 'make docs' now ...
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc'
creating doc/NEWS
creating doc/NEWS.pdf
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
creating doc/manual/R-FAQ.html
creating doc/manual/version.texi
creating doc/manual/R-admin.html
creating doc/manual/R-data.html
creating doc/manual/R-exts.html
creating doc/manual/R-intro.html
creating doc/manual/R-ints.html
creating doc/manual/R-lang.html
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/html'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/html'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
installing parsed Rd
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
building/updating package metadata ...
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
writing package indices
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
building all R object docs
  converting help for package 'base'
    Arithmetic                              html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/Arithmetic.Rd:158: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    AsIs                                    html  
    Bessel                                  html  
    CallExternal                            html  
    Colon                                   html  
    Comparison                              html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/Comparison.Rd:101: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    Constants                               html  
    Control                                 html  
    Cstack_info                             html  
    DateTimeClasses                         html  
    Dates                                   html  
    Defunct                                 html  
    Deprecated                              html  
    Encoding                                html  
    EnvVar                                  html  
    Extract                                 html  
    Extract.data.frame                      html  
    Extract.factor                          html  
    Extremes                                html  
    Foreign-internal                        html  
    Foreign                                 html  
    Hyperbolic                              html  
    ISOdatetime                             html  
    Internal                                html  
    InternalMethods                         html  
    La_library                              html  
    La_version                              html  
    Last.value                              html  
    Log                                     html  
    Logic                                   html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/Logic.Rd:110: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    LongVectors                             html  
    MathFun                                 html  
    Memory-limits                           html  
    Memory                                  html  
    NA                                      html  
    NULL                                    html  
    NumericConstants                        html  
    Ops.Date                                html  
    Paren                                   html  
    Platform                                html  
    Primitive                               html  
    Quotes                                  html  
    Random-user                             html  
    Random                                  html  
    RdUtils                                 html  
    Recall                                  html  
    Reserved                                html  
    Rhome                                   html  
    Round                                   html  
    Special                                 html  
    Startup                                 html  
    Syntax                                  html  
    Sys.getenv                              html  
    Sys.getpid                              html  
    Sys.glob                                html  
    Sys.info                                html  
    Sys.localeconv                          html  
    Sys.readlink                            html  
    Sys.setFileTime                         html  
    Sys.setenv                              html  
    Sys.sleep                               html  
    Sys.time                                html  
    Sys.which                               html  
    Trig                                    html  
    UseMethod                               html  
    Vectorize                               html  
    Version                                 html  
    abbreviate                              html  
    agrep                                   html  
    all                                     html  
    all.equal                               html  
    allnames                                html  
    any                                     html  
    aperm                                   html  
    append                                  html  
    apply                                   html  
    args                                    html  
    array                                   html  
    as.Date                                 html  
    as.POSIXlt                              html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/as.POSIXlt.Rd:141: file link 'format.POSIXlt' in package 'base' does not exist and so has been treated as a topic
    as.data.frame                           html  
    as.environment                          html  
    as.function                             html  
    asplit                                  html  
    assign                                  html  
    assignOps                               html  
    attach                                  html  
    attr                                    html  
    attributes                              html  
    autoload                                html  
    backsolve                               html  
    base-defunct                            html  
    base-deprecated                         html  
    base-internal                           html  
    base-package                            html  
    basename                                html  
    bincode                                 html  
    bindenv                                 html  
    bitwise                                 html  
    body                                    html  
    bquote                                  html  
    browser                                 html  
    browserText                             html  
    builtins                                html  
    by                                      html  
    c                                       html  
    call                                    html  
    callCC                                  html  
    capabilities                            html  
    cat                                     html  
    cbind                                   html  
    char.expand                             html  
    character                               html  
    charmatch                               html  
    chartr                                  html  
    chkDots                                 html  
    chol                                    html  
    chol2inv                                html  
    class                                   html  
    col                                     html  
    colSums                                 html  
    colnames                                html  
    commandArgs                             html  
    comment                                 html  
    complex                                 html  
    conditions                              html  
    conflicts                               html  
    connections                             html  
    contributors                            html  
    copyright                               html  
    crossprod                               html  
    cumsum                                  html  
    curlGetHeaders                          html  
    cut.POSIXt                              html  
    cut                                     html  
    data.class                              html  
    data.frame                              html  
    data.matrix                             html  
    dataframeHelpers                        html  
    date                                    html  
    dcf                                     html  
    debug                                   html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/debug.Rd:73: file link 'isRematched' in package 'methods' does not exist and so has been treated as a topic
    delayedAssign                           html  
    deparse                                 html  
    deparseOpts                             html  
    det                                     html  
    detach                                  html  
    dev                                     html  
    diag                                    html  
    diff                                    html  
    difftime                                html  
    dim                                     html  
    dimnames                                html  
    do.call                                 html  
    dontCheck                               html  
    dots                                    html  
    double                                  html  
    dput                                    html  
    drop                                    html  
    droplevels                              html  
    dump                                    html  
    duplicated                              html  
    dynload                                 html  
    eapply                                  html  
    eigen                                   html  
    encodeString                            html  
    environment                             html  
    eval                                    html  
    exists                                  html  
    expand.grid                             html  
    expression                              html  
    extSoftVersion                          html  
    factor                                  html  
    file.access                             html  
    file.choose                             html  
    file.info                               html  
    file.path                               html  
    file.show                               html  
    files                                   html  
    files2                                  html  
    find.package                            html  
    findInterval                            html  
    force                                   html  
    forceAndCall                            html  
    formals                                 html  
    format                                  html  
    format.info                             html  
    format.pval                             html  
    formatDL                                html  
    formatc                                 html  
    function                                html  
    funprog                                 html  
    gc                                      html  
    gc.time                                 html  
    gctorture                               html  
    get                                     html  
    getCallingDLL                           html  
    getDLLRegisteredRoutines                html  
    getLoadedDLLs                           html  
    getNativeSymbolInfo                     html  
    gettext                                 html  
    getwd                                   html  
    gl                                      html  
    grep                                    html  
    grepRaw                                 html  
    groupGeneric                            html  
    grouping                                html  
    gzcon                                   html  
    hexmode                                 html  
    iconv                                   html  
    icuSetCollate                           html  
    identical                               html  
    identity                                html  
    ifelse                                  html  
    integer                                 html  
    interaction                             html  
    interactive                             html  
    invisible                               html  
    is.finite                               html  
    is.function                             html  
    is.language                             html  
    is.object                               html  
    is.recursive                            html  
    is.single                               html  
    is.unsorted                             html  
    isR                                     html  
    isS4                                    html  
    isSymmetric                             html  
    jitter                                  html  
    kappa                                   html  
    kronecker                               html  
    l10n_info                               html  
    labels                                  html  
    lapply                                  html  
    lazyload                                html  
    length                                  html  
    lengths                                 html  
    levels                                  html  
    libPaths                                html  
    libcurlVersion                          html  
    library                                 html  
    library.dynam                           html  
    license                                 html  
    list                                    html  
    list.files                              html  
    list2env                                html  
    load                                    html  
    locales                                 html  
    logical                                 html  
    lower.tri                               html  
    ls                                      html  
    make.names                              html  
    make.unique                             html  
    mapply                                  html  
    margin.table                            html  
    mat.or.vec                              html  
    match                                   html  
    match.arg                               html  
    match.call                              html  
    match.fun                               html  
    matmult                                 html  
    matrix                                  html  
    maxCol                                  html  
    mean                                    html  
    memCompress                             html  
    memlimits                               html  
    memory.profile                          html  
    merge                                   html  
    message                                 html  
    missing                                 html  
    mode                                    html  
    name                                    html  
    names                                   html  
    nargs                                   html  
    nchar                                   html  
    nlevels                                 html  
    noquote                                 html  
    norm                                    html  
    normalizePath                           html  
    notyet                                  html  
    nrow                                    html  
    ns-dblcolon                             html  
    ns-hooks                                html  
    ns-internal                             html  
    ns-load                                 html  
    ns-reflect                              html  
    ns-topenv                               html  
    numeric                                 html  
    numeric_version                         html  
    octmode                                 html  
    on.exit                                 html  
    options                                 html  
    order                                   html  
    outer                                   html  
    parse                                   html  
    paste                                   html  
    path.expand                             html  
    pcre_config                             html  
    pmatch                                  html  
    polyroot                                html  
    pos.to.env                              html  
    pretty                                  html  
    print                                   html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/print.Rd:86: file link '.print.via.format' in package 'tools' does not exist and so has been treated as a topic
    print.dataframe                         html  
    print.default                           html  
    prmatrix                                html  
    proc.time                               html  
    prod                                    html  
    prop.table                              html  
    pushBack                                html  
    qr                                      html  
    qraux                                   html  
    quit                                    html  
    range                                   html  
    rank                                    html  
    rapply                                  html  
    raw                                     html  
    rawConnection                           html  
    rawConversion                           html  
    readBin                                 html  
    readChar                                html  
    readLines                               html  
    readRDS                                 html  
    readRenviron                            html  
    readline                                html  
    reg.finalizer                           html  
    regex                                   html  
    regmatches                              html  
    rep                                     html  
    replace                                 html  
    rev                                     html  
    rle                                     html  
    rm                                      html  
    round.POSIXt                            html  
    row                                     html  
    row.names                               html  
    rowsum                                  html  
    sQuote                                  html  
    sample                                  html  
    save                                    html  
    scale                                   html  
    scan                                    html  
    search                                  html  
    seek                                    html  
    seq.Date                                html  
    seq.POSIXt                              html  
    seq                                     html  
    sequence                                html  
    serialize                               html  
    setTimeLimit                            html  
    sets                                    html  
    shQuote                                 html  
    showConnections                         html  
    sign                                    html  
    sink                                    html  
    slice.index                             html  
    slotOp                                  html  
    socketSelect                            html  
    solve                                   html  
    sort                                    html  
    source                                  html  
    split                                   html  
    sprintf                                 html  
    srcfile                                 html  
    standardGeneric                         html  
    startsWith                              html  
    stop                                    html  
    stopifnot                               html  
    strptime                                html  
    strrep                                  html  
    strsplit                                html  
    strtoi                                  html  
    strtrim                                 html  
    structure                               html  
    strwrap                                 html  
    subset                                  html  
    substitute                              html  
    substr                                  html  
    sum                                     html  
    summary                                 html  
    svd                                     html  
    sweep                                   html  
    switch                                  html  
    sys.parent                              html  
    sys.source                              html  
    system                                  html  
    system.file                             html  
    system.time                             html  
    system2                                 html  
    t                                       html  
    table                                   html  
    tabulate                                html  
    tapply                                  html  
    taskCallback                            html  
    taskCallbackManager                     html  
    taskCallbackNames                       html  
    tempfile                                html  
    textconnections                         html  
    tilde                                   html  
    timezones                               html  
    toString                                html  
    trace                                   html  
    traceback                               html  
    tracemem                                html  
    transform                               html  
    trimws                                  html  
    try                                     html  
    typeof                                  html  
    unique                                  html  
    unlink                                  html  
    unlist                                  html  
    unname                                  html  
    userhooks                               html  
    utf8Conversion                          html  
    validUTF8                               html  
    vector                                  html  
    warning                                 html  
    warnings                                html  
    weekday.POSIXt                          html  
    which                                   html  
    which.min                               html  
    with                                    html  
    withVisible                             html  
    write                                   html  
    writeLines                              html  
    xtfrm                                   html  
    zMachine                                html  
    zScript                                 html  
    zapsmall                                html  
    zpackages                               html  
    zutils                                  html  
    Signals                                 html  
  converting help for package 'tools'
    CRANtools                               html  
    HTMLheader                              html  
    HTMLlinks                               html  
    QC                                      html  
    Rcmd                                    html  
    Rd2HTML                                 html  
    Rd2txt_options                          html  
    RdTextFilter                            html  
    Rdiff                                   html  
    Rdindex                                 html  
    Rdutils                                 html  
    SweaveTeXFilter                         html  
    add_datalist                            html  
    assertCondition                         html  
    bibstyle                                html  
    buildVignette                           html  
    buildVignettes                          html  
    charsets                                html  
    checkFF                                 html  
    checkMD5sums                            html  
    checkPoFiles                            html  
    checkRd                                 html  
    checkRdaFiles                           html  
    checkTnF                                html  
    checkVignettes                          html  
    check_packages_in_dir                   html  
Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/tools/man/check_packages_in_dir.Rd:123: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    codoc                                   html  
    compactPDF                              html  
    delimMatch                              html  
    dependsOnPkgs                           html  
    encoded                                 html  
    fileutils                               html  
    find_gs_cmd                             html  
    getVignetteInfo                         html  
    loadRdMacros                            html  
    makeLazyLoading                         html  
    make_translations_pkg                   html  
    makevars                                html  
    md5sum                                  html  
    package_dependencies                    html  
    package_native_routine_registration_skeleton
                                            html  
    parseLatex                              html  
    parse_Rd                                html  
    print.via.format                        html  
    pskill                                  html  
    psnice                                  html  
    read.00Index                            html  
    showNonASCII                            html  
    startDynamicHelp                        html  
    testInstalledPackage                    html  
    texi2dvi                                html  
    toHTML                                  html  
    toRd                                    html  
    toTitleCase                             html  
    tools-defunct                           html  
    tools-deprecated                        html  
    tools-package                           html  
    undoc                                   html  
    updatePACKAGES                          html  
    update_pkg_po                           html  
    vignetteEngine                          html  
    vignetteInfo                            html  
    writePACKAGES                           html  
    xgettext                                html  
  converting help for package 'utils'
    BATCH                                   html  
    COMPILE                                 html  
    DLL.version                             html  
    INSTALL                                 html  
    LINK                                    html  
    PkgUtils                                html  
    Question                                html  
    REMOVE                                  html  
    RHOME                                   html  
    RShowDoc                                html  
    RSiteSearch                             html  
    Rconsole                                html  
    Rprof                                   html  
    Rprofmem                                html  
    Rscript                                 html  
    Rtangle                                 html  
    RweaveLatex                             html  
    SHLIB                                   html  
    Sweave                                  html  
    SweaveSyntConv                          html  
    SweaveUtils                             html  
    URLencode                               html  
    View                                    html  
    adist                                   html  
    alarm                                   html  
    apropos                                 html  
    aregexec                                html  
    arrangeWindows                          html  
    askYesNo                                html  
    aspell-utils                            html  
    aspell                                  html  
    available.packages                      html  
    bibentry                                html  
    browseEnv                               html  
    browseURL                               html  
    browseVignettes                         html  
    bug.report                              html  
    capture.output                          html  
    changedFiles                            html  
    choose.dir                              html  
    choose.files                            html  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citEntry                                html  
    citation                                html  
    cite                                    html  
    clipboard                               html  
    close.socket                            html  
    combn                                   html  
    compareVersion                          html  
    contrib.url                             html  
    count.fields                            html  
    create.post                             html  
    data                                    html  
    dataentry                               html  
    debugcall                               html  
    debugger                                html  
    demo                                    html  
    download.file                           html  
    download.packages                       html  
    edit                                    html  
    edit.data.frame                         html  
    example                                 html  
    file.edit                               html  
    filetest                                html  
    findLineNum                             html  
    fix                                     html  
    flush.console                           html  
    format                                  html  
    getAnywhere                             html  
    getFromNamespace                        html  
    getParseData                            html  
    getS3method                             html  
    getWindowsHandle                        html  
    getWindowsHandles                       html  
    glob2rx                                 html  
    globalVariables                         html  
    hasName                                 html  
    head                                    html  
    help                                    html  
    help.request                            html  
    help.search                             html  
    help.start                              html  
    hsearch-utils                           html  
    install.packages                        html  
    installed.packages                      html  
    isS3method                              html  
    isS3stdGen                              html  
    localeToCharset                         html  
    ls_str                                  html  
    maintainer                              html  
    make.packages.html                      html  
    make.socket                             html  
    memory.size                             html  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    html  
    nsl                                     html  
    object.size                             html  
    package.skeleton                        html  
    packageDescription                      html  
    packageName                             html  
    packageStatus                           html  
    page                                    html  
    person                                  html  
    process.events                          html  
    prompt                                  html  
    promptData                              html  
    promptPackage                           html  
    rcompgen                                html  
    read.DIF                                html  
    read.fortran                            html  
    read.fwf                                html  
    read.socket                             html  
    read.table                              html  
    readRegistry                            html  
    recover                                 html  
    relist                                  html  
    remove.packages                         html  
    removeSource                            html  
    roman                                   html  
    rtags                                   html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         html  
    setWindowTitle                          html  
    shortPathName                           html  
    sourceutils                             html  
    stack                                   html  
    str                                     html  
    strcapture                              html  
    summaryRprof                            html  
    tar                                     html  
    toLatex                                 html  
    txtProgressBar                          html  
    type.convert                            html  
    untar                                   html  
    unzip                                   html  
    update.packages                         html  
    url.show                                html  
    utils-defunct                           html  
    utils-deprecated                        html  
    utils-package                           html  
    vignette                                html  
    warnErrList                             html  
    winDialog                               html  
    winMenus                                html  
    winProgressBar                          html  
    winextras                               html  
    write.table                             html  
    zip                                     html  
  converting help for package 'grDevices'
    Devices                                 html  
    Hershey                                 html  
    Japanese                                html  
    Type1Font                               html  
    adjustcolor                             html  
    as.graphicsAnnot                        html  
    as.raster                               html  
    axisTicks                               html  
    boxplot.stats                           html  
    bringToTop                              html  
    cairo                                   html  
    check.options                           html  
    chull                                   html  
    cm                                      html  
    col2rgb                                 html  
    colorRamp                               html  
    colors                                  html  
    contourLines                            html  
    convertColor                            html  
    densCols                                html  
    dev                                     html  
    dev.capabilities                        html  
    dev.capture                             html  
    dev.flush                               html  
    dev.interactive                         html  
    dev.size                                html  
    dev2                                    html  
    dev2bitmap                              html  
    devAskNewPage                           html  
    embedFonts                              html  
    extendrange                             html  
    getGraphicsEvent                        html  
    grDevices-package                       html  
    grSoftVersion                           html  
    gray                                    html  
    gray.colors                             html  
    hcl                                     html  
    hsv                                     html  
    make.rgb                                html  
    msgWindow                               html  
    n2mfrow                                 html  
    nclass                                  html  
    palette                                 html  
    palettes                                html  
    pdf                                     html  
    pdf.options                             html  
    pictex                                  html  
    plotmath                                html  
    postscript                              html  
    postscriptFonts                         html  
    pretty.Date                             html  
    ps.options                              html  
    quartz                                  html  
    quartzFonts                             html  
    recordGraphics                          html  
    recordplot                              html  
    rgb                                     html  
    rgb2hsv                                 html  
    trans3d                                 html  
    windows                                 html  
    windows.options                         html  
    windowsFonts                            html  
    x11                                     html  
    x11Fonts                                html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    savePlot                                html  
  converting help for package 'graphics'
    abline                                  html  
    arrows                                  html  
    assocplot                               html  
    axTicks                                 html  
    axis.POSIXct                            html  
    axis                                    html  
    barplot                                 html  
    box                                     html  
    boxplot                                 html  
    boxplot.matrix                          html  
    bxp                                     html  
    cdplot                                  html  
    clip                                    html  
    contour                                 html  
    convertXY                               html  
    coplot                                  html  
    curve                                   html  
    dotchart                                html  
    filled.contour                          html  
    fourfoldplot                            html  
    frame                                   html  
    graphics-defunct                        html  
    graphics-package                        html  
    grid                                    html  
    hist.POSIXt                             html  
    hist                                    html  
    identify                                html  
    image                                   html  
    layout                                  html  
    legend                                  html  
    lines                                   html  
    locator                                 html  
    matplot                                 html  
    mosaicplot                              html  
    mtext                                   html  
    pairs                                   html  
    panel.smooth                            html  
    par                                     html  
    persp                                   html  
    pie                                     html  
    plot                                    html  
    plot.dataframe                          html  
    plot.default                            html  
    plot.design                             html  
    plot.factor                             html  
    plot.formula                            html  
    plot.raster                             html  
    plot.table                              html  
    plot.window                             html  
    plot.xy                                 html  
    plothistogram                           html  
    points                                  html  
    polygon                                 html  
    polypath                                html  
    rasterImage                             html  
    rect                                    html  
    rug                                     html  
    screen                                  html  
    segments                                html  
    smoothScatter                           html  
    spineplot                               html  
    stars                                   html  
    stem                                    html  
    stripchart                              html  
    strwidth                                html  
    sunflowerplot                           html  
    symbols                                 html  
    text                                    html  
    title                                   html  
    units                                   html  
    xspline                                 html  
    zAxis                                   html  
  converting help for package 'stats'
    AIC                                     html  
    ARMAacf                                 html  
    ARMAtoMA                                html  
    Beta                                    html  
    Binomial                                html  
    Cauchy                                  html  
    Chisquare                               html  
    Distributions                           html  
    Exponential                             html  
    Fdist                                   html  
    GammaDist                               html  
    Geometric                               html  
    HoltWinters                             html  
    Hypergeometric                          html  
    IQR                                     html  
    KalmanLike                              html  
    Logistic                                html  
    Lognormal                               html  
    Multinom                                html  
    NLSstAsymptotic                         html  
    NLSstClosestX                           html  
    NLSstLfAsymptote                        html  
    NLSstRtAsymptote                        html  
    NegBinomial                             html  
    Normal                                  html  
    Poisson                                 html  
    SSD                                     html  
    SSasymp                                 html  
    SSasympOff                              html  
    SSasympOrig                             html  
    SSbiexp                                 html  
    SSfol                                   html  
    SSfpl                                   html  
    SSgompertz                              html  
    SSlogis                                 html  
    SSmicmen                                html  
    SSweibull                               html  
    SignRank                                html  
    StructTS                                html  
    TDist                                   html  
    Tukey                                   html  
    TukeyHSD                                html  
    Uniform                                 html  
    Weibull                                 html  
    Wilcoxon                                html  
    acf                                     html  
    acf2AR                                  html  
    add1                                    html  
    addmargins                              html  
    aggregate                               html  
    alias                                   html  
    anova                                   html  
    anova.glm                               html  
    anova.lm                                html  
    anova.mlm                               html  
    ansari.test                             html  
    aov                                     html  
    approxfun                               html  
    ar                                      html  
    ar.ols                                  html  
    arima                                   html  
    arima.sim                               html  
    arima0                                  html  
    as.hclust                               html  
    asOneSidedFormula                       html  
    ave                                     html  
    bandwidth                               html  
    bartlett.test                           html  
    binom.test                              html  
    biplot                                  html  
    biplot.princomp                         html  
    birthday                                html  
    box.test                                html  
    cancor                                  html  
    case.names                              html  
    checkMFClasses                          html  
    chisq.test                              html  
    cmdscale                                html  
    coef                                    html  
    complete.cases                          html  
    confint                                 html  
    constrOptim                             html  
    contrast                                html  
    contrasts                               html  
    convolve                                html  
    cophenetic                              html  
    cor                                     html  
    cor.test                                html  
    cov.wt                                  html  
    cpgram                                  html  
    cutree                                  html  
    decompose                               html  
    delete.response                         html  
    dendrapply                              html  
    dendrogram                              html  
    density                                 html  
    deriv                                   html  
    deviance                                html  
    df.residual                             html  
    diffinv                                 html  
    dist                                    html  
    dummy.coef                              html  
    ecdf                                    html  
    eff.aovlist                             html  
    effects                                 html  
    embed                                   html  
    expand.model.frame                      html  
    extractAIC                              html  
    factanal                                html  
    factor.scope                            html  
    family                                  html  
    fft                                     html  
    filter                                  html  
    fisher.test                             html  
    fitted.values                           html  
    fivenum                                 html  
    fligner.test                            html  
    formula                                 html  
    formula.nls                             html  
    friedman.test                           html  
    ftable                                  html  
    ftable.formula                          html  
    getInitial                              html  
    glm                                     html  
    glm.control                             html  
    glm.summaries                           html  
    hclust                                  html  
    heatmap                                 html  
    identify.hclust                         html  
    influence.measures                      html  
    integrate                               html  
    interaction.plot                        html  
    is.empty                                html  
    isoreg                                  html  
    kernapply                               html  
    kernel                                  html  
    kmeans                                  html  
    kruskal.test                            html  
    ks.test                                 html  
    ksmooth                                 html  
    lag                                     html  
    lag.plot                                html  
    line                                    html  
    listof                                  html  
    lm                                      html  
    lm.influence                            html  
    lm.summaries                            html  
    lmfit                                   html  
    loadings                                html  
    loess                                   html  
    loess.control                           html  
    logLik                                  html  
    loglin                                  html  
    lowess                                  html  
    ls.diag                                 html  
    ls.print                                html  
    lsfit                                   html  
    mad                                     html  
    mahalanobis                             html  
    make.link                               html  
    makepredictcall                         html  
    manova                                  html  
    mantelhaen.test                         html  
    mauchly.test                            html  
    mcnemar.test                            html  
    median                                  html  
    medpolish                               html  
    model.extract                           html  
    model.frame                             html  
    model.matrix                            html  
    model.tables                            html  
    monthplot                               html  
    mood.test                               html  
    na.action                               html  
    na.contiguous                           html  
    na.fail                                 html  
    nafns                                   html  
    naprint                                 html  
    nextn                                   html  
    nlm                                     html  
    nlminb                                  html  
    nls                                     html  
    nls.control                             html  
    nobs                                    html  
    numericDeriv                            html  
    offset                                  html  
    oneway.test                             html  
    optim                                   html  
    optimize                                html  
    order.dendrogram                        html  
    p.adjust                                html  
    pairwise.prop.test                      html  
    pairwise.t.test                         html  
    pairwise.table                          html  
    pairwise.wilcox.test                    html  
    plot.HoltWinters                        html  
    plot.acf                                html  
    plot.density                            html  
    plot.isoreg                             html  
    plot.lm                                 html  
    plot.ppr                                html  
    plot.profile.nls                        html  
    plot.spec                               html  
    plot.stepfun                            html  
    plot.ts                                 html  
    poisson.test                            html  
    poly                                    html  
    power                                   html  
    power.anova.test                        html  
    power.prop.test                         html  
    power.t.test                            html  
    pp.test                                 html  
    ppoints                                 html  
    ppr                                     html  
    prcomp                                  html  
    predict.HoltWinters                     html  
    predict                                 html  
    predict.arima                           html  
    predict.glm                             html  
    predict.lm                              html  
    predict.loess                           html  
    predict.nls                             html  
    predict.smooth.spline                   html  
    preplot                                 html  
    princomp                                html  
    print.power.htest                       html  
    print.ts                                html  
    printCoefmat                            html  
    profile                                 html  
    profile.nls                             html  
    proj                                    html  
    prop.test                               html  
    prop.trend.test                         html  
    qqnorm                                  html  
    quade.test                              html  
    quantile                                html  
    r2dtable                                html  
    rWishart                                html  
    read.ftable                             html  
    rect.hclust                             html  
    relevel                                 html  
    reorder.dendrogram                      html  
    reorder.factor                          html  
    replications                            html  
    reshape                                 html  
    residuals                               html  
    runmed                                  html  
    scatter.smooth                          html  
    screeplot                               html  
    sd                                      html  
    se.contrast                             html  
    selfStart                               html  
    setNames                                html  
    shapiro.test                            html  
    sigma                                   html  
    simulate                                html  
    smooth                                  html  
    smooth.spline                           html  
    smoothEnds                              html  
    sortedXyData                            html  
    spec.ar                                 html  
    spec.pgram                              html  
    spec.taper                              html  
    spectrum                                html  
    splinefun                               html  
    start                                   html  
    stat.anova                              html  
    stats-defunct                           html  
    stats-deprecated                        html  
    stats-package                           html  
    step                                    html  
    stepfun                                 html  
    stl                                     html  
    stlmethods                              html  
    summary.aov                             html  
    summary.glm                             html  
    summary.lm                              html  
    summary.manova                          html  
    summary.nls                             html  
    summary.princomp                        html  
    supsmu                                  html  
    symnum                                  html  
    t.test                                  html  
    termplot                                html  
    terms                                   html  
    terms.formula                           html  
    terms.object                            html  
    time                                    html  
    toeplitz                                html  
    ts-methods                              html  
    ts                                      html  
    ts.plot                                 html  
    ts.union                                html  
    tsSmooth                                html  
    tsdiag                                  html  
    tsp                                     html  
    uniroot                                 html  
    update                                  html  
    update.formula                          html  
    var.test                                html  
    varimax                                 html  
    vcov                                    html  
    weighted.mean                           html  
    weighted.residuals                      html  
    weights                                 html  
    wilcox.test                             html  
    window                                  html  
    xtabs                                   html  
    zC                                      html  
  converting help for package 'datasets'
    AirPassengers                           html  
    BJsales                                 html  
    BOD                                     html  
    ChickWeight                             html  
    DNase                                   html  
    EuStockMarkets                          html  
    Formaldehyde                            html  
    HairEyeColor                            html  
    Harman23.cor                            html  
    Harman74.cor                            html  
    Indometh                                html  
    InsectSprays                            html  
    JohnsonJohnson                          html  
    LakeHuron                               html  
    LifeCycleSavings                        html  
    Loblolly                                html  
    Nile                                    html  
    Orange                                  html  
    OrchardSprays                           html  
    PlantGrowth                             html  
    Puromycin                               html  
    Theoph                                  html  
    Titanic                                 html  
    ToothGrowth                             html  
    UCBAdmissions                           html  
    UKDriverDeaths                          html  
    UKLungDeaths                            html  
    UKgas                                   html  
    USAccDeaths                             html  
    USArrests                               html  
    USJudgeRatings                          html  
    USPersonalExpenditure                   html  
    VADeaths                                html  
    WWWusage                                html  
    WorldPhones                             html  
    ability.cov                             html  
    airmiles                                html  
    airquality                              html  
    anscombe                                html  
    attenu                                  html  
    attitude                                html  
    austres                                 html  
    beavers                                 html  
    cars                                    html  
    chickwts                                html  
    co2                                     html  
    crimtab                                 html  
    datasets-package                        html  
    discoveries                             html  
    esoph                                   html  
    euro                                    html  
    eurodist                                html  
    faithful                                html  
    freeny                                  html  
    infert                                  html  
    iris                                    html  
    islands                                 html  
    lh                                      html  
    longley                                 html  
    lynx                                    html  
    morley                                  html  
    mtcars                                  html  
    nhtemp                                  html  
    nottem                                  html  
    npk                                     html  
    occupationalStatus                      html  
    precip                                  html  
    presidents                              html  
    pressure                                html  
    quakes                                  html  
    randu                                   html  
    rivers                                  html  
    rock                                    html  
    sleep                                   html  
    stackloss                               html  
    state                                   html  
    sunspot.month                           html  
    sunspot.year                            html  
    sunspots                                html  
    swiss                                   html  
    treering                                html  
    trees                                   html  
    uspop                                   html  
    volcano                                 html  
    warpbreaks                              html  
    women                                   html  
    zCO2                                    html  
  converting help for package 'methods'
    BasicClasses                            html  
    Classes                                 html  
    Classes_Details                         html  
    Documentation                           html  
    EmptyMethodsList-class                  html  
    EnvironmentClass                        html  
    GenericFunctions                        html  
    Introduction                            html  
    LanguageClasses                         html  
    LinearMethodsList-class                 html  
    MethodDefinition-class                  html  
    MethodSupport                           html  
    MethodWithNext-class                    html  
    Methods                                 html  
    MethodsList-class                       html  
    MethodsList                             html  
    Methods_Details                         html  
    Methods_for_Nongenerics                 html  
    Methods_for_S3                          html  
    NextMethod                              html  
    ObjectsWithPackage-class                html  
    RClassUtils                             html  
    RMethodUtils                            html  
    S3Part                                  html  
    S4groupGeneric                          html  
    SClassExtension-class                   html  
    StructureClasses                        html  
    TraceClasses                            html  
    as                                      html  
    callGeneric                             html  
    canCoerce                               html  
    cbind2                                  html  
    className                               html  
    classRepresentation-class               html  
    classesToAM                             html  
    dotsMethods                             html  
    evalSource                              html  
    findClass                               html  
    findMethods                             html  
    fixPrevious                             html  
    genericFunction-class                   html  
    getClass                                html  
    getMethod                               html  
    getPackageName                          html  
    hasArg                                  html  
    implicitGeneric                         html  
    inheritedSlotNames                      html  
    initialize-methods                      html  
    is                                      html  
    isSealedMethod                          html  
    languageEl                              html  
    localRefClass                           html  
    method.skeleton                         html  
    methodUtilities                         html  
    methods-defunct                         html  
    methods-deprecated                      html  
    methods-package                         html  
    new                                     html  
    nonStructure-class                      html  
    promptClass                             html  
    promptMethods                           html  
    refClass                                html  
    removeMethod                            html  
    representation                          html  
    selectSuperClasses                      html  
    setAs                                   html  
    setClass                                html  
    setClassUnion                           html  
    setGeneric                              html  
    setGroupGeneric                         html  
    setIs                                   html  
    setLoadActions                          html  
    setMethod                               html  
    setOldClass                             html  
    setSClass                               html  
    show                                    html  
    showMethods                             html  
    signature-class                         html  
    slot                                    html  
    stdRefClass                             html  
    substituteDirect                        html  
    testInheritedMethods                    html  
    validObject                             html  
    zBasicFunsList                          html  
  converting help for package 'grid'
    Grid                                    html  
    absolute.size                           html  
    arrow                                   html  
    calcStringMetric                        html  
    current.viewport                        html  
    dataViewport                            html  
    depth                                   html  
    deviceLoc                               html  
    drawDetails                             html  
    editDetails                             html  
    explode                                 html  
    gEdit                                   html  
    gPath                                   html  
    getNames                                html  
    gpar                                    html  
    grid-defunct                            html  
    grid-internal                           html  
    grid-package                            html  
    grid.DLapply                            html  
    grid.add                                html  
    grid.bezier                             html  
    grid.cap                                html  
    grid.circle                             html  
    grid.clip                               html  
    grid.convert                            html  
    grid.copy                               html  
    grid.curve                              html  
    grid.delay                              html  
    grid.display.list                       html  
    grid.draw                               html  
    grid.edit                               html  
    grid.force                              html  
    grid.frame                              html  
    grid.function                           html  
    grid.get                                html  
    grid.grab                               html  
    grid.grep                               html  
    grid.grill                              html  
    grid.grob                               html  
    grid.layout                             html  
    grid.lines                              html  
    grid.locator                            html  
    grid.ls                                 html  
    grid.move.to                            html  
    grid.newpage                            html  
    grid.null                               html  
    grid.pack                               html  
    grid.path                               html  
    grid.place                              html  
    grid.plot.and.legend                    html  
    grid.points                             html  
    grid.polygon                            html  
    grid.pretty                             html  
    grid.raster                             html  
    grid.record                             html  
    grid.rect                               html  
    grid.refresh                            html  
    grid.remove                             html  
    grid.reorder                            html  
    grid.roundrect                          html  
    grid.segments                           html  
    grid.set                                html  
    grid.show.layout                        html  
    grid.show.viewport                      html  
    grid.text                               html  
    grid.xaxis                              html  
    grid.xspline                            html  
    grid.yaxis                              html  
    grobCoords                              html  
    grobName                                html  
    grobWidth                               html  
    grobX                                   html  
    legendGrob                              html  
    makeContent                             html  
    plotViewport                            html  
    resolveRasterSize                       html  
    showGrob                                html  
    showViewport                            html  
    stringWidth                             html  
    unit                                    html  
    unit.c                                  html  
    unit.length                             html  
    unit.pmin                               html  
    unit.rep                                html  
    valid.just                              html  
    validDetails                            html  
    viewport                                html  
    viewports                               html  
    vpPath                                  html  
    widthDetails                            html  
    xDetails                                html  
    xsplinePoints                           html  
  converting help for package 'splines'
    asVector                                html  
    backSpline                              html  
    bs                                      html  
    interpSpline                            html  
    ns                                      html  
    periodicSpline                          html  
    polySpline                              html  
    predict.bSpline                         html  
    predict.bs                              html  
    splineDesign                            html  
    splineKnots                             html  
    splineOrder                             html  
    splines-package                         html  
    xyVector                                html  
  converting help for package 'stats4'
    coef-methods                            html  
    confint-methods                         html  
    logLik-methods                          html  
    mle-class                               html  
    mle                                     html  
    plot-methods                            html  
    profile-methods                         html  
    profile.mle-class                       html  
    show-methods                            html  
    stats4-package                          html  
    summary-methods                         html  
    summary.mle-class                       html  
    update-methods                          html  
    vcov-methods                            html  
  converting help for package 'tcltk'
    TclInterface                            html  
    TkCommands                              html  
    TkWidgetcmds                            html  
    TkWidgets                               html  
    tclServiceMode                          html  
    tcltk-defunct                           html  
    tcltk-package                           html  
    tkProgressBar                           html  
    tkStartGUI                              html  
    tk_choose.dir                           html  
    tk_choose.files                         html  
    tk_messageBox                           html  
    tk_select.list                          html  
    tkpager                                 html  
  converting help for package 'compiler'
    compile                                 html  
  converting help for package 'parallel'
    RngStream                               html  
    clusterApply                            html  
    detectCores                             html  
    makeCluster                             html  
    parallel-package                        html  
    splitIndices                            html  
    children                                html  
    mcaffinity                              html  
    mcfork                                  html  
    mclapply                                html  
    mcparallel                              html  
    pvec                                    html  
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/Recommended'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpRquRz4/R.INSTALL30c4339d5478/MASS/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c MASS.c -o MASS.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lqs.c -o lqs.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpRquRz4/R.INSTALL30c4339d5478/MASS/src'
installing to /builddir/build/BUILD/R-3.6.0/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MASS'
    finding HTML links ... done
    Aids2                                   html  
    Animals                                 html  
    Boston                                  html  
    Cars93                                  html  
    Cushings                                html  
    DDT                                     html  
    GAGurine                                html  
    Insurance                               html  
    MASS-internal                           html  
    Melanoma                                html  
    Null                                    html  
    OME                                     html  
    Pima.tr                                 html  
    Rabbit                                  html  
    Rubber                                  html  
    SP500                                   html  
    Sitka                                   html  
    Sitka89                                 html  
    Skye                                    html  
    Traffic                                 html  
    UScereal                                html  
    UScrime                                 html  
    VA                                      html  
    abbey                                   html  
    accdeaths                               html  
    addterm                                 html  
    anorexia                                html  
    anova.negbin                            html  
    area                                    html  
    bacteria                                html  
    bandwidth.nrd                           html  
    bcv                                     html  
    beav1                                   html  
    beav2                                   html  
    biopsy                                  html  
    birthwt                                 html  
    boxcox                                  html  
    cabbages                                html  
    caith                                   html  
    cats                                    html  
    cement                                  html  
    chem                                    html  
    con2tr                                  html  
    confint                                 html  
    contr.sdif                              html  
    coop                                    html  
    corresp                                 html  
    cov.rob                                 html  
    cov.trob                                html  
    cpus                                    html  
    crabs                                   html  
    deaths                                  html  
    denumerate                              html  
    dose.p                                  html  
    drivers                                 html  
    dropterm                                html  
    eagles                                  html  
    epil                                    html  
    eqscplot                                html  
    farms                                   html  
    fgl                                     html  
    fitdistr                                html  
    forbes                                  html  
    fractions                               html  
    galaxies                                html  
    gamma.dispersion                        html  
    gamma.shape.glm                         html  
    gehan                                   html  
    genotype                                html  
    geyser                                  html  
    gilgais                                 html  
    ginv                                    html  
    glm.convert                             html  
    glm.nb                                  html  
    glmmPQL                                 html  
    hills                                   html  
    hist.scott                              html  
    housing                                 html  
    huber                                   html  
    hubers                                  html  
    immer                                   html  
    isoMDS                                  html  
    kde2d                                   html  
    lda                                     html  
    ldahist                                 html  
    leuk                                    html  
    lm.gls                                  html  
    lm.ridge                                html  
    loglm                                   html  
    loglm1                                  html  
    logtrans                                html  
    lqs                                     html  
    mammals                                 html  
    mca                                     html  
    mcycle                                  html  
    menarche                                html  
    michelson                               html  
    minn38                                  html  
    motors                                  html  
    muscle                                  html  
    mvrnorm                                 html  
    negative.binomial                       html  
    newcomb                                 html  
    nlschools                               html  
    npk                                     html  
    npr1                                    html  
    oats                                    html  
    painters                                html  
    pairs.lda                               html  
    parcoord                                html  
    petrol                                  html  
    phones                                  html  
    plot.lda                                html  
    plot.mca                                html  
    plot.profile                            html  
    polr                                    html  
    predict.glmmPQL                         html  
    predict.lda                             html  
    predict.lqs                             html  
    predict.mca                             html  
    predict.qda                             html  
    profile.glm                             html  
    qda                                     html  
    quine                                   html  
    rational                                html  
    renumerate                              html  
    rlm                                     html  
    rms.curv                                html  
    rnegbin                                 html  
    road                                    html  
    rotifer                                 html  
    sammon                                  html  
    ships                                   html  
    shoes                                   html  
    shrimp                                  html  
    shuttle                                 html  
    snails                                  html  
    stdres                                  html  
    steam                                   html  
    stepAIC                                 html  
    stormer                                 html  
    studres                                 html  
    summary.loglm                           html  
    summary.negbin                          html  
    summary.rlm                             html  
    survey                                  html  
    synth.tr                                html  
    theta.md                                html  
    topo                                    html  
    truehist                                html  
    ucv                                     html  
    waders                                  html  
    whiteside                               html  
    width.SJ                                html  
    write.matrix                            html  
    wtloss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Making 'packages.html' ... done
begin installing recommended package lattice
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/Rtmp3fXh5U/R.INSTALL3125196abe2/lattice/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c threeDplot.c -o threeDplot.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o lattice.so init.o threeDplot.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmp3fXh5U/R.INSTALL3125196abe2/lattice/src'
installing to /builddir/build/BUILD/R-3.6.0/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lattice'
    finding HTML links ... done
    Lattice                                 html  
    Rows                                    html  
    USMortality                             html  
    axis.default                            html  
    banking                                 html  
    barchart.table                          html  
    barley                                  html  
    cloud                                   html  
    draw.colorkey                           html  
    draw.key                                html  
    environmental                           html  
    ethanol                                 html  
    histogram                               html  
    interaction                             html  
    lattice.options                         html  
    latticeParseFormula                     html  
    level.colors                            html  
    levelplot                               html  
    llines                                  html  
    lset                                    html  
    make.groups                             html  
    melanoma                                html  
    oneway                                  html  
    packet.panel.default                    html  
    panel.axis                              html  
    panel.barchart                          html  
    panel.bwplot                            html  
    panel.cloud                             html  
    panel.densityplot                       html  
    panel.dotplot                           html  
    panel.functions                         html  
    panel.histogram                         html  
    panel.levelplot                         html  
    panel.loess                             html  
    panel.number                            html  
    panel.pairs                             html  
    panel.parallel                          html  
    panel.qqmath                            html  
    panel.qqmathline                        html  
    panel.smoothScatter                     html  
    panel.spline                            html  
    panel.stripplot                         html  
    panel.superpose                         html  
    panel.violin                            html  
    panel.xyplot                            html  
    prepanel.default                        html  
    prepanel.functions                      html  
    print.trellis                           html  
    qq                                      html  
    qqmath                                  html  
    rfs                                     html  
    shingles                                html  
    simpleKey                               html  
    simpleTheme                             html  
    singer                                  html  
    splom                                   html  
    strip.default                           html  
    tmd                                     html  
    trellis.device                          html  
    trellis.object                          html  
    trellis.par.get                         html  
    update.trellis                          html  
    utilities.3d                            html  
    xyplot                                  html  
    xyplot.ts                               html  
** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done
begin installing recommended package Matrix
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Csparse.c -o Csparse.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c TMatrix_as.c -o TMatrix_as.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Tsparse.c -o Tsparse.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Mutils.c -o Mutils.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chm_common.c -o chm_common.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
                  ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cs_utils.c -o cs_utils.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dense.c -o dense.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgCMatrix.c -o dgCMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgTMatrix.c -o dgTMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgeMatrix.c -o dgeMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dpoMatrix.c -o dpoMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dppMatrix.c -o dppMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dsCMatrix.c -o dsCMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dsyMatrix.c -o dsyMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dspMatrix.c -o dspMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dtCMatrix.c -o dtCMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dtTMatrix.c -o dtTMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dtrMatrix.c -o dtrMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dtpMatrix.c -o dtpMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c factorizations.c -o factorizations.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ldense.c -o ldense.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgCMatrix.c -o lgCMatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sparseQR.c -o sparseQR.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c abIndex.c -o abIndex.o
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD/Source'
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD/Source'
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/SuiteSparse_config'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD/Lib'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop.3':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop.3':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD'
( cd Source ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD/Source'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c colamd_global.c -o colamd_global.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c colamd.c -o colamd.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD'
( cd Source ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD/Source'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
make[5]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/AMD'
make[4]: Entering directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER  -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/builddir/build/BUILD/R-3.6.0/lib -lRlapack -L/builddir/build/BUILD/R-3.6.0/lib -lRblas -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/src'
installing to /builddir/build/BUILD/R-3.6.0/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix'
** help
*** installing help indices
  converting help for package 'Matrix'
    finding HTML links ... done
    BunchKaufman-methods                    html  
    CAex                                    html  
    CHMfactor-class                         html  
    Cholesky-class                          html  
    Cholesky                                html  
    CsparseMatrix-class                     html  
    Diagonal                                html  
    Hilbert                                 html  
    KNex                                    html  
    KhatriRao                               html  
    LU-class                                html  
    Matrix-class                            html  
    Matrix                                  html  
    MatrixClass                             html  
    MatrixFactorization-class               html  
    RsparseMatrix-class                     html  
    Schur-class                             html  
    Schur                                   html  
    SparseM-conv                            html  
    Subassign-methods                       html  
    TsparseMatrix-class                     html  
    USCounties                              html  
    Xtrct-methods                           html  
    abIndex-class                           html  
Rd warning: /tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
    abIseq                                  html  
    all-methods                             html  
    all.equal-methods                       html  
    atomicVector-class                      html  
    band                                    html  
    bandSparse                              html  
    bdiag                                   html  
    boolean-matprod                         html  
    cBind                                   html  
    chol                                    html  
    chol2inv-methods                        html  
    colSums                                 html  
    compMatrix-class                        html  
    condest                                 html  
    dMatrix-class                           html  
    ddenseMatrix-class                      html  
    ddiMatrix-class                         html  
    denseMatrix-class                       html  
    dgCMatrix-class                         html  
    dgRMatrix-class                         html  
    dgTMatrix-class                         html  
    dgeMatrix-class                         html  
    diagU2N                                 html  
    diagonalMatrix-class                    html  
    dpoMatrix-class                         html  
    drop0                                   html  
    dsCMatrix-class                         html  
    dsRMatrix-class                         html  
    dsparseMatrix-class                     html  
    dsyMatrix-class                         html  
    dtCMatrix-class                         html  
    dtRMatrix-class-def                     html  
    dtpMatrix-class                         html  
    dtrMatrix-class                         html  
    expand                                  html  
    expm                                    html  
    externalFormats                         html  
    facmul                                  html  
    forceSymmetric                          html  
    formatSparseM                           html  
    generalMatrix-class                     html  
    graph2T                                 html  
    image-methods                           html  
Rd warning: /tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/man/image-methods.Rd:81: file link 'get.gpar' in package 'grid' does not exist and so has been treated as a topic
    indMatrix-class                         html  
    index-class                             html  
    invPerm                                 html  
    is.na-methods                           html  
    is.null.DN                              html  
    isSymmetric-methods                     html  
    isTriangular                            html  
    kronecker-methods                       html  
    ldenseMatrix-class                      html  
    ldiMatrix-class                         html  
    lgeMatrix-class                         html  
    lsparseMatrix-classes                   html  
    lsyMatrix-class                         html  
    ltrMatrix-class                         html  
    lu                                      html  
    matrix-products                         html  
Rd warning: /tmp/RtmpPSMwah/R.INSTALL31a950cb0f6b/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic
    nMatrix-class                           html  
    ndenseMatrix-class                      html  
    nearPD                                  html  
    ngeMatrix-class                         html  
    nnzero                                  html  
    norm                                    html  
    nsparseMatrix-classes                   html  
    nsyMatrix-class                         html  
    ntrMatrix-class                         html  
    number-class                            html  
    pMatrix-class                           html  
    printSpMatrix                           html  
    qr-methods                              html  
    rankMatrix                              html  
    rcond                                   html  
    rep2abI                                 html  
    replValue-class                         html  
    rleDiff-class                           html  
    rsparsematrix                           html  
    solve-methods                           html  
    spMatrix                                html  
    sparse.model.matrix                     html  
    sparseLU-class                          html  
    sparseMatrix-class                      html  
    sparseMatrix                            html  
    sparseQR-class                          html  
    sparseVector-class                      html  
    sparseVector                            html  
    symmetricMatrix-class                   html  
    symmpart                                html  
    triangularMatrix-class                  html  
    uniqTsparse                             html  
    unpack                                  html  
    unused-classes                          html  
    updown                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
begin installing recommended package nlme
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/src'
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c chol.f -o chol.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c corStruct.c -o corStruct.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gnls.c -o gnls.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c matrix.c -o matrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nlme.c -o nlme.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nlmefit.c -o nlmefit.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pdMat.c -o pdMat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pythag.c -o pythag.o
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c rs.f -o rs.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/src'
installing to /builddir/build/BUILD/R-3.6.0/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nlme'
    finding HTML links ... done
    ACF                                     html  
    ACF.gls                                 html  
    ACF.lme                                 html  
    Alfalfa                                 html  
    Assay                                   html  
    BodyWeight                              html  
    Cefamandole                             html  
    Coef                                    html  
    Covariate                               html  
    Covariate.varFunc                       html  
    Dialyzer                                html  
    Dim                                     html  
    Dim.corSpatial                          html  
    Dim.corStruct                           html  
    Dim.pdMat                               html  
    Earthquake                              html  
    Extract.pdMat                           html  
    Fatigue                                 html  
    Gasoline                                html  
    Glucose                                 html  
    Glucose2                                html  
    Gun                                     html  
    IGF                                     html  
    Initialize                              html  
    Initialize.corStruct                    html  
    Initialize.glsStruct                    html  
    Initialize.lmeStruct                    html  
    Initialize.reStruct                     html  
    Initialize.varFunc                      html  
    LDEsysMat                               html  
    Machines                                html  
    MathAchSchool                           html  
    MathAchieve                             html  
    Matrix                                  html  
    Matrix.pdMat                            html  
    Matrix.reStruct                         html  
    Meat                                    html  
    Milk                                    html  
    Muscle                                  html  
    Names                                   html  
    Names.formula                           html  
    Names.pdBlocked                         html  
    Names.pdMat                             html  
    Names.reStruct                          html  
    Nitrendipene                            html  
    Oats                                    html  
    Orthodont                               html  
    Ovary                                   html  
    Oxboys                                  html  
    Oxide                                   html  
    PBG                                     html  
    Phenobarb                               html  
    Pixel                                   html  
    Quinidine                               html  
    Rail                                    html  
    RatPupWeight                            html  
    Relaxin                                 html  
    Remifentanil                            html  
    Soybean                                 html  
    Spruce                                  html  
    Tetracycline1                           html  
    Tetracycline2                           html  
    VarCorr                                 html  
    Variogram                               html  
    Variogram.corExp                        html  
    Variogram.corGaus                       html  
    Variogram.corLin                        html  
    Variogram.corRatio                      html  
    Variogram.corSpatial                    html  
    Variogram.corSpher                      html  
    Variogram.default                       html  
    Variogram.gls                           html  
    Variogram.lme                           html  
    Wafer                                   html  
    Wheat                                   html  
    Wheat2                                  html  
    allCoef                                 html  
    anova.gls                               html  
    anova.lme                               html  
    as.matrix.corStruct                     html  
    as.matrix.pdMat                         html  
    as.matrix.reStruct                      html  
    asOneFormula                            html  
    asTable                                 html  
    augPred                                 html  
    balancedGrouped                         html  
    bdf                                     html  
    coef.corStruct                          html  
    coef.gnls                               html  
    coef.lmList                             html  
    coef.lme                                html  
    coef.modelStruct                        html  
    coef.pdMat                              html  
    coef.reStruct                           html  
    coef.varFunc                            html  
    collapse                                html  
    collapse.groupedData                    html  
    compareFits                             html  
    comparePred                             html  
    corAR1                                  html  
    corARMA                                 html  
    corCAR1                                 html  
    corClasses                              html  
    corCompSymm                             html  
    corExp                                  html  
    corFactor                               html  
    corFactor.corStruct                     html  
    corGaus                                 html  
    corLin                                  html  
    corMatrix                               html  
    corMatrix.corStruct                     html  
    corMatrix.pdMat                         html  
    corMatrix.reStruct                      html  
    corNatural                              html  
    corRatio                                html  
    corSpatial                              html  
    corSpher                                html  
    corSymm                                 html  
    ergoStool                               html  
    fdHess                                  html  
    fitted.glsStruct                        html  
    fitted.gnlsStruct                       html  
    fitted.lmList                           html  
    fitted.lme                              html  
    fitted.lmeStruct                        html  
    fitted.nlmeStruct                       html  
    fixed.effects                           html  
    fixef.lmList                            html  
    formula.pdBlocked                       html  
    formula.pdMat                           html  
    formula.reStruct                        html  
    gapply                                  html  
    getCovariate                            html  
    getCovariate.corStruct                  html  
    getCovariate.data.frame                 html  
    getCovariate.varFunc                    html  
    getCovariateFormula                     html  
    getData                                 html  
    getData.gls                             html  
    getData.lmList                          html  
    getData.lme                             html  
    getGroups                               html  
    getGroups.corStruct                     html  
    getGroups.data.frame                    html  
    getGroups.gls                           html  
    getGroups.lmList                        html  
    getGroups.lme                           html  
    getGroups.varFunc                       html  
    getGroupsFormula                        html  
    getResponse                             html  
    getResponseFormula                      html  
    getVarCov                               html  
    gls-internal                            html  
    gls                                     html  
    glsControl                              html  
    glsObject                               html  
    glsStruct                               html  
    gnls                                    html  
    gnlsControl                             html  
    gnlsObject                              html  
    gnlsStruct                              html  
    groupedData                             html  
    gsummary                                html  
    intervals                               html  
    intervals.gls                           html  
    intervals.lmList                        html  
    intervals.lme                           html  
    isBalanced                              html  
    isInitialized                           html  
    lmList                                  html  
    lmList.groupedData                      html  
    lme                                     html  
    lme.groupedData                         html  
    lme.lmList                              html  
    lmeControl                              html  
    lmeObject                               html  
    lmeStruct                               html  
    logDet                                  html  
    logDet.corStruct                        html  
    logDet.pdMat                            html  
    logDet.reStruct                         html  
    logLik.corStruct                        html  
    logLik.glsStruct                        html  
    logLik.gnls                             html  
    logLik.gnlsStruct                       html  
    logLik.lmList                           html  
    logLik.lme                              html  
    logLik.lmeStruct                        html  
    logLik.reStruct                         html  
    logLik.varFunc                          html  
    model.matrix.reStruct                   html  
    needUpdate                              html  
    needUpdate.modelStruct                  html  
    nlme                                    html  
    nlme.nlsList                            html  
    nlmeControl                             html  
    nlmeObject                              html  
    nlmeStruct                              html  
    nlsList                                 html  
    nlsList.selfStart                       html  
    pairs.compareFits                       html  
    pairs.lmList                            html  
    pairs.lme                               html  
    pdBlocked                               html  
    pdClasses                               html  
    pdCompSymm                              html  
    pdConstruct                             html  
    pdConstruct.pdBlocked                   html  
    pdDiag                                  html  
    pdFactor                                html  
    pdFactor.reStruct                       html  
    pdIdent                                 html  
    pdLogChol                               html  
    pdMat                                   html  
    pdMatrix                                html  
    pdMatrix.reStruct                       html  
    pdNatural                               html  
    pdSymm                                  html  
    phenoModel                              html  
    plot.ACF                                html  
    plot.Variogram                          html  
    plot.augPred                            html  
    plot.compareFits                        html  
    plot.gls                                html  
    plot.intervals.lmList                   html  
Rd warning: /tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    plot.lmList                             html  
    plot.lme                                html  
    plot.nffGroupedData                     html  
    plot.nfnGroupedData                     html  
    plot.nmGroupedData                      html  
    plot.ranef.lmList                       html  
    plot.ranef.lme                          html  
Rd warning: /tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpPMM8VP/R.INSTALL3670397e585c/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    pooledSD                                html  
    predict.gls                             html  
    predict.gnls                            html  
    predict.lmList                          html  
    predict.lme                             html  
    predict.nlme                            html  
    print.summary.pdMat                     html  
    print.varFunc                           html  
    qqnorm.gls                              html  
    qqnorm.lme                              html  
    quinModel                               html  
    random.effects                          html  
    ranef.lmList                            html  
    ranef.lme                               html  
    reStruct                                html  
    recalc                                  html  
    recalc.corStruct                        html  
    recalc.modelStruct                      html  
    recalc.reStruct                         html  
    recalc.varFunc                          html  
    residuals.gls                           html  
    residuals.glsStruct                     html  
    residuals.gnlsStruct                    html  
    residuals.lmList                        html  
    residuals.lme                           html  
    residuals.lmeStruct                     html  
    residuals.nlmeStruct                    html  
    simulate.lme                            html  
    solve.pdMat                             html  
    solve.reStruct                          html  
    splitFormula                            html  
    summary.corStruct                       html  
    summary.gls                             html  
    summary.lmList                          html  
    summary.lme                             html  
    summary.modelStruct                     html  
    summary.nlsList                         html  
    summary.pdMat                           html  
    summary.varFunc                         html  
    update.modelStruct                      html  
    update.varFunc                          html  
    varClasses                              html  
    varComb                                 html  
    varConstPower                           html  
    varExp                                  html  
    varFixed                                html  
    varFunc                                 html  
    varIdent                                html  
    varPower                                html  
    varWeights                              html  
    varWeights.glsStruct                    html  
    varWeights.lmeStruct                    html  
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
begin installing recommended package survival
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmptVJ5sl/R.INSTALL37283a7f7e1e/survival/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agexact.c -o agexact.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agfit4.c -o agfit4.o
agfit4.c: In function 'agfit4':
agfit4.c:575:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized]
                     if (tstop[p] < dtime) break; /* no more to add */
                        ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agfit5.c -o agfit5.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agmart.c -o agmart.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agmart2.c -o agmart2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agmart3.c -o agmart3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agscore.c -o agscore.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agsurv3.c -o agsurv3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agsurv4.c -o agsurv4.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c agsurv5.c -o agsurv5.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chinv2.c -o chinv2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chinv3.c -o chinv3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cholesky2.c -o cholesky2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cholesky3.c -o cholesky3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cholesky5.c -o cholesky5.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chsolve2.c -o chsolve2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chsolve3.c -o chsolve3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chsolve5.c -o chsolve5.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c concordance1.c -o concordance1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c concordance3.c -o concordance3.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cox_Rcallback.c -o cox_Rcallback.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxcount1.c -o coxcount1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxdetail.c -o coxdetail.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxexact.c -o coxexact.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxfit5.c -o coxfit5.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxfit6.c -o coxfit6.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxmart.c -o coxmart.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxmart2.c -o coxmart2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxph_wtest.c -o coxph_wtest.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxsafe.c -o coxsafe.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxscho.c -o coxscho.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxscore.c -o coxscore.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dmatrix.c -o dmatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c doloop.c -o doloop.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c finegray.c -o finegray.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gchol.c -o gchol.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c norisk.c -o norisk.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pyears1.c -o pyears1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pyears2.c -o pyears2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pyears3b.c -o pyears3b.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pystep.c -o pystep.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survConcordance.c -o survConcordance.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survdiff2.c -o survdiff2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survfit4.c -o survfit4.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survfitci.c -o survfitci.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survfitkm.c -o survfitkm.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survpenal.c -o survpenal.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survreg6.c -o survreg6.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survreg7.c -o survreg7.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survregc1.c -o survregc1.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survregc2.c -o survregc2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c survsplit.c -o survsplit.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c tmerge.c -o tmerge.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmptVJ5sl/R.INSTALL37283a7f7e1e/survival/src'
installing to /builddir/build/BUILD/R-3.6.0/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survival'
    finding HTML links ... done
    Surv                                    html  
    Survmethods                             html  
    aareg                                   html  
    aeqSurv                                 html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    cipoisson                               html  
Rd warning: /tmp/RtmptVJ5sl/R.INSTALL37283a7f7e1e/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmptVJ5sl/R.INSTALL37283a7f7e1e/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    concordance                             html  
    concordancefit                          html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    diabetic                                html  
    dsurvreg                                html  
    finegray                                html  
    flchain                                 html  
    frailty                                 html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  html  
    levels.Surv                             html  
    lines.survfit                           html  
    logLik.coxph                            html  
    logan                                   html  
    lung                                    html  
    mgus                                    html  
    mgus2                                   html  
    model.frame.coxph                       html  
    model.matrix.coxph                      html  
    myeloid                                 html  
    neardate                                html  
    nwtco                                   html  
    ovarian                                 html  
    pbc                                     html  
    pbcseq                                  html  
    plot.aareg                              html  
    plot.cox.zph                            html  
    plot.survfit                            html  
    predict.coxph                           html  
    predict.survreg                         html  
    print.aareg                             html  
    print.summary.coxph                     html  
    print.summary.survexp                   html  
    print.summary.survfit                   html  
    print.survfit                           html  
    pspline                                 html  
    pyears                                  html  
    quantile.survfit                        html  
    ratetable                               html  
    ratetableDate                           html  
    rats                                    html  
    rats2                                   html  
    reliability                             html  
    residuals.coxph                         html  
    residuals.survreg                       html  
    retinopathy                             html  
    rhDNase                                 html  
    ridge                                   html  
    solder                                  html  
    stanford2                               html  
    statefig                                html  
    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.pyears                          html  
    summary.survexp                         html  
    summary.survfit                         html  
    survConcordance-deprecated              html  
    survSplit                               html  
    survdiff                                html  
    survexp                                 html  
    survexp.fit                             html  
    survexp.object                          html  
    survexp.us                              html  
    survfit                                 html  
    survfit.coxph                           html  
    survfit.formula                         html  
    survfit.matrix                          html  
    survfit.object                          html  
    survfitcoxph.fit                        html  
    survival-internal                       html  
    survobrien                              html  
    survreg                                 html  
    survreg.control                         html  
    survreg.distributions                   html  
    survreg.object                          html  
    survregDtest                            html  
    tcut                                    html  
    tmerge                                  html  
    tobin                                   html  
    transplant                              html  
    udca                                    html  
    untangle.specials                       html  
    uspop2                                  html  
    vcov.coxph                              html  
    veteran                                 html  
    xtfrm.Surv                              html  
    yates                                   html  
    yates_setup                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done
begin installing recommended package boot
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'boot'
    finding HTML links ... done
    EEF.profile                             html  
    Imp.Estimates                           html  
    abc.ci                                  html  
    acme                                    html  
    aids                                    html  
    aircondit                               html  
    amis                                    html  
    aml                                     html  
    beaver                                  html  
    bigcity                                 html  
    boot-practicals                         html  
    boot                                    html  
    boot.array                              html  
    boot.ci                                 html  
    brambles                                html  
    breslow                                 html  
    calcium                                 html  
    cane                                    html  
    capability                              html  
    catsM                                   html  
    cav                                     html  
    cd4                                     html  
    cd4.nested                              html  
    censboot                                html  
    channing                                html  
    claridge                                html  
    cloth                                   html  
    co.transfer                             html  
    coal                                    html  
    control                                 html  
    corr                                    html  
    cum3                                    html  
    cv.glm                                  html  
    darwin                                  html  
    dogs                                    html  
    downs.bc                                html  
    ducks                                   html  
    empinf                                  html  
    envelope                                html  
    exp.tilt                                html  
    fir                                     html  
    freq.array                              html  
    frets                                   html  
    glm.diag                                html  
    glm.diag.plots                          html  
    gravity                                 html  
    hirose                                  html  
    imp.weights                             html  
    inv.logit                               html  
    islay                                   html  
    jack.after.boot                         html  
    k3.linear                               html  
    linear.approx                           html  
    lines.saddle.distn                      html  
    logit                                   html  
    manaus                                  html  
    melanoma                                html  
    motor                                   html  
    neuro                                   html  
    nitrofen                                html  
    nodal                                   html  
    norm.ci                                 html  
    nuclear                                 html  
    paulsen                                 html  
    plot.boot                               html  
    poisons                                 html  
    polar                                   html  
    print.boot                              html  
    print.bootci                            html  
    print.saddle.distn                      html  
    print.simplex                           html  
    remission                               html  
    saddle                                  html  
    saddle.distn                            html  
    saddle.distn.object                     html  
    salinity                                html  
    simplex                                 html  
    simplex.object                          html  
    smooth.f                                html  
    sunspot                                 html  
    survival                                html  
    tau                                     html  
    tilt.boot                               html  
    tsboot                                  html  
    tuna                                    html  
    urine                                   html  
    var.linear                              html  
    wool                                    html  
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done
begin installing recommended package cluster
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c clara.c -o clara.o
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c daisy.f -o daisy.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dysta.f -o dysta.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fanny.c -o fanny.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mona.c -o mona.o
mona.c: In function 'clmona_':
mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ner[k] = nelbb;
          ^
mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lcc, nelbb;
       ^
mona.c:235:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized]
      km = ka + jtel2;
      ^
mona.c:218:24: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if(verbose) Rprintf("  for(j ..) -> jma=%d, jtel(.,z) = (%d, %d)", jma, jtel, jtelz);
                        ^
mona.c:274:11: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized]
  lava[km] = jma;
           ^
mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
   jtel = c + d;
        ^
mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized]
   jtelz = a + b;
         ^
mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pam.c -o pam.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sildist.c -o sildist.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c spannel.c -o spannel.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c twins.c -o twins.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/src'
installing to /builddir/build/BUILD/R-3.6.0/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cluster'
    finding HTML links ... done
    agnes                                   html  
    agnes.object                            html  
    agriculture                             html  
    animals                                 html  
    bannerplot                              html  
    chorSub                                 html  
    clara                                   html  
    clara.object                            html  
    clusGap                                 html  
    clusplot.default                        html  
Rd warning: /tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
    diana                                   html  
    dissimilarity.object                    html  
    ellipsoidhull                           html  
Rd warning: /tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    fanny                                   html  
    fanny.object                            html  
    flower                                  html  
    lower.to.upper.tri.inds                 html  
    mona                                    html  
    mona.object                             html  
    pam                                     html  
    pam.object                              html  
    partition.object                        html  
    plantTraits                             html  
    plot.agnes                              html  
Rd warning: /tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic
    plot.diana                              html  
    plot.mona                               html  
    plot.partition                          html  
    pltree                                  html  
    pluton                                  html  
    predict.ellipsoid                       html  
    print.agnes                             html  
    print.clara                             html  
    print.diana                             html  
    print.dissimilarity                     html  
Rd warning: /tmp/RtmpgWDmSi/R.INSTALL38cb2fa17075/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic
    print.fanny                             html  
    print.mona                              html  
    print.pam                               html  
    ruspini                                 html  
    silhouette                              html  
    sizeDiss                                html  
    summary.agnes                           html  
    summary.clara                           html  
    summary.diana                           html  
    summary.mona                            html  
    summary.pam                             html  
    twins.object                            html  
    volume.ellipsoid                        html  
    votes.repub                             html  
    xclara                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
Making 'packages.html' ... done
begin installing recommended package codetools
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'codetools'
    finding HTML links ... done
    checkUsage                              html  
    codetools                               html  
    findGlobals                             html  
    showTree                                html  
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
Making 'packages.html' ... done
begin installing recommended package foreign
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/Rtmpg3Pqaa/R.INSTALL39584ab46032/foreign/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c R_systat.c -o R_systat.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rdbfread.c -o Rdbfread.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c Rdbfwrite.c -o Rdbfwrite.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c SASxport.c -o SASxport.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c avl.c -o avl.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbfopen.c -o dbfopen.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c file-handle.c -o file-handle.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c format.c -o format.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c minitab.c -o minitab.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pfm-read.c -o pfm-read.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sfm-read.c -o sfm-read.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c spss.c -o spss.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stataread.c -o stataread.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmpg3Pqaa/R.INSTALL39584ab46032/foreign/src'
installing to /builddir/build/BUILD/R-3.6.0/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'foreign'
    finding HTML links ... done
    lookup.xport                            html  
    read.S                                  html  
    read.arff                               html  
    read.dbf                                html  
    read.dta                                html  
    read.epiinfo                            html  
    read.mtp                                html  
    read.octave                             html  
    read.spss                               html  
    read.ssd                                html  
    read.systat                             html  
    read.xport                              html  
    write.arff                              html  
    write.dbf                               html  
    write.dta                               html  
    write.foreign                           html  
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done
begin installing recommended package KernSmooth
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/Rtmph2z9Bv/R.INSTALL39c14f06cac8/KernSmooth/src'
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c blkest.f -o blkest.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c cp.f -o cp.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dgedi.f -o dgedi.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dgefa.f -o dgefa.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c dgesl.f -o dgesl.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c linbin.f -o linbin.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c linbin2D.f -o linbin2D.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c locpoly.f -o locpoly.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c rlbin.f -o rlbin.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c sdiag.f -o sdiag.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -I/usr/lib/gfortran/modules  -c sstdiag.f -o sstdiag.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -L/builddir/build/BUILD/R-3.6.0/lib -lRblas -lgfortran -lm -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmph2z9Bv/R.INSTALL39c14f06cac8/KernSmooth/src'
installing to /builddir/build/BUILD/R-3.6.0/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KernSmooth'
    finding HTML links ... done
    bkde                                    html  
    bkde2D                                  html  
    bkfe                                    html  
    dpih                                    html  
    dpik                                    html  
    dpill                                   html  
    locpoly                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done
begin installing recommended package rpart
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpCwXrW5/R.INSTALL3a086813c638/rpart/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c anova.c -o anova.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c anovapred.c -o anovapred.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c branch.c -o branch.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bsplit.c -o bsplit.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c choose_surg.c -o choose_surg.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fix_cp.c -o fix_cp.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c free_tree.c -o free_tree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gini.c -o gini.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c graycode.c -o graycode.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c insert_split.c -o insert_split.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c make_cp_list.c -o make_cp_list.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c make_cp_table.c -o make_cp_table.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mysort.c -o mysort.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nodesplit.c -o nodesplit.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c partition.c -o partition.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c poisson.c -o poisson.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pred_rpart.c -o pred_rpart.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c print_tree.c -o print_tree.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpart.c -o rpart.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpart_callback.c -o rpart_callback.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpartexp.c -o rpartexp.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpartexp2.c -o rpartexp2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpcountup.c -o rpcountup.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpmatrix.c -o rpmatrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rundown.c -o rundown.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rundown2.c -o rundown2.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c surrogate.c -o surrogate.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c usersplit.c -o usersplit.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c xpred.c -o xpred.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c xval.c -o xval.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpCwXrW5/R.INSTALL3a086813c638/rpart/src'
installing to /builddir/build/BUILD/R-3.6.0/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rpart'
    finding HTML links ... done
    car.test.frame                          html  
    car90                                   html  
    cu.summary                              html  
    kyphosis                                html  
    labels.rpart                            html  
    meanvar.rpart                           html  
    na.rpart                                html  
    path.rpart                              html  
    plot.rpart                              html  
    plotcp                                  html  
    post.rpart                              html  
    predict.rpart                           html  
    print.rpart                             html  
    printcp                                 html  
    prune.rpart                             html  
    residuals.rpart                         html  
    rpart-internal                          html  
    rpart                                   html  
    rpart.control                           html  
    rpart.exp                               html  
    rpart.object                            html  
    rsq.rpart                               html  
    snip.rpart                              html  
    solder.balance                          html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
begin installing recommended package class
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpCfMUeQ/R.INSTALL3ab4d0cbbc0/class/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c class.c -o class.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o class.so class.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpCfMUeQ/R.INSTALL3ab4d0cbbc0/class/src'
installing to /builddir/build/BUILD/R-3.6.0/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'class'
    finding HTML links ... done
    SOM                                     html  
    batchSOM                                html  
    condense                                html  
    knn                                     html  
    knn.cv                                  html  
    knn1                                    html  
    lvq1                                    html  
    lvq2                                    html  
    lvq3                                    html  
    lvqinit                                 html  
    lvqtest                                 html  
    multiedit                               html  
    olvq1                                   html  
    reduce.nn                               html  
    somgrid                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done
begin installing recommended package nnet
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpMlQw76/R.INSTALL3ada3da6da79/nnet/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c nnet.c -o nnet.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o nnet.so nnet.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpMlQw76/R.INSTALL3ada3da6da79/nnet/src'
installing to /builddir/build/BUILD/R-3.6.0/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nnet'
    finding HTML links ... done
    class.ind                               html  
    multinom                                html  
    nnet.Hess                               html  
    nnet                                    html  
    predict.nnet                            html  
    which.is.max                            html  
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
begin installing recommended package spatial
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/Rtmpjqv0yd/R.INSTALL3b004375b0ba/spatial/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c krc.c -o krc.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pps.c -o pps.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o spatial.so init.o krc.o pps.o -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmpjqv0yd/R.INSTALL3b004375b0ba/spatial/src'
installing to /builddir/build/BUILD/R-3.6.0/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatial'
    finding HTML links ... done
    Kaver                                   html  
    Kenvl                                   html  
    Kfn                                     html  
    Psim                                    html  
    SSI                                     html  
    Strauss                                 html  
    anova.trls                              html  
    correlogram                             html  
    expcov                                  html  
    ppgetregion                             html  
    ppinit                                  html  
    pplik                                   html  
    ppregion                                html  
    predict.trls                            html  
    prmat                                   html  
    semat                                   html  
    surf.gls                                html  
    surf.ls                                 html  
    trls.influence                          html  
    trmat                                   html  
    variogram                               html  
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done
begin installing recommended package mgcv
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory `/tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/src'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c coxph.c -o coxph.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c discrete.c -o discrete.o
discrete.c: In function 'indReduce':
discrete.c:86:32: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double Wij,*Cq,*Aq,*Cq1,*ws,*wl;
                                ^
discrete.c:86:28: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double Wij,*Cq,*Aq,*Cq1,*ws,*wl;
                            ^
discrete.c: In function 'XWXijs':
discrete.c:1177:26: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
           F77_CALL(dgemm)(&trans,&ntrans,p+im,p+jm,m+jm,&done,D,m+jm,X+off[jm],m+jm,&dzero,XWX+r*p[im]+c*p[jm]*(ptrdiff_t)nxwx,&nxwx);
                          ^
discrete.c:1175:26: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized]
           F77_CALL(dgemm)(&trans,&ntrans,p+im,p+jm,m+im,&done,X+off[im],m+im,C,m+im,&dzero,XWX+r*p[im]+c*p[jm]*(ptrdiff_t)nxwx,&nxwx);
                          ^
discrete.c:834:12: warning: 'W' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
            ^
discrete.c:833:13: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
   double x,*wl,*dXi,*dXj,*pdXj,*Xt,*Xi,*Xj,done=1.0,dzero=0.0,*Cq,*Dq,
             ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gdi.c -o gdi.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c init.c -o init.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c magic.c -o magic.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mat.c -o mat.o
mat.c: In function 'chol_down':
mat.c:1747:9: warning: unused variable 'j' [-Wunused-variable]
   int i,j,n1;
         ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c matrix.c -o matrix.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c misc.c -o misc.o
misc.c: In function 'tweedious':
misc.c:401:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
misc.c:485:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mvn.c -o mvn.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qp.c -o qp.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c soap.c -o soap.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/builddir/build/BUILD/R-3.6.0/lib -lRlapack -L/builddir/build/BUILD/R-3.6.0/lib -lRblas -lgfortran -lm -fopenmp -L/builddir/build/BUILD/R-3.6.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/src'
installing to /builddir/build/BUILD/R-3.6.0/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mgcv'
    finding HTML links ... done
    Beta                                    html  
    FFdes                                   html  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
    Sl.initial.repara                       html  
    Sl.repara                               html  
    Sl.setup                                html  
    Tweedie                                 html  
    anova.gam                               html  
    bam                                     html  
Rd warning: /tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/man/bam.Rd:14: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/man/bam.Rd:129: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/man/bam.Rd:188: file link 'makeForkCluster' in package 'parallel' does not exist and so has been treated as a topic
    bam.update                              html  
    bandchol                                html  
    bug.reports.mgcv                        html  
    cSplineDes                              html  
    chol.down                               html  
    choose.k                                html  
    columb                                  html  
    concurvity                              html  
    coxph                                   html  
    coxpht                                  html  
    dDeta                                   html  
    exclude.too.far                         html  
    extract.lme.cov                         html  
    family.mgcv                             html  
    fix.family.link                         html  
    fixDependence                           html  
    formXtViX                               html  
    formula.gam                             html  
    fs.test                                 html  
    full.score                              html  
    gam                                     html  
    gam.check                               html  
    gam.control                             html  
    gam.convergence                         html  
    gam.fit                                 html  
    gam.fit3                                html  
    gam.fit5.post.proc                      html  
    gam.models                              html  
    gam.outer                               html  
    gam.reparam                             html  
    gam.scale                               html  
    gam.selection                           html  
    gam.side                                html  
    gam.vcomp                               html  
    gam2objective                           html  
    gamObject                               html  
    gamSim                                  html  
    gamlss.etamu                            html  
    gamlss.gH                               html  
    gamm                                    html  
    gaulss                                  html  
    get.var                                 html  
    gevlss                                  html  
    ginla                                   html  
    identifiability                         html  
    in.out                                  html  
    inSide                                  html  
    influence.gam                           html  
    initial.sp                              html  
    interpret.gam                           html  
    jagam                                   html  
    k.check                                 html  
    ldTweedie                               html  
    ldetS                                   html  
    linear.functional.terms                 html  
    logLik.gam                              html  
    ls.size                                 html  
    magic                                   html  
    magic.post.proc                         html  
    mgcv-FAQ                                html  
    mgcv-package                            html  
    mgcv-parallel                           html  
Rd warning: /tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/man/mgcv-parallel.Rd:11: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
    mini.roots                              html  
    missing.data                            html  
    model.matrix.gam                        html  
    mono.con                                html  
    mroot                                   html  
    multinom                                html  
    mvn                                     html  
    negbin                                  html  
    new.name                                html  
    notExp                                  html  
    notExp2                                 html  
    null.space.dimension                    html  
    ocat                                    html  
    one.se.rule                             html  
    pcls                                    html  
    pdIdnot                                 html  
    pdTens                                  html  
    pen.edf                                 html  
    place.knots                             html  
    plot.gam                                html  
    polys.plot                              html  
    predict.bam                             html  
Rd warning: /tmp/RtmpyVQpJC/R.INSTALL3b401588af20/mgcv/man/predict.bam.Rd:76: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    predict.gam                             html  
    print.gam                               html  
    qq.gam                                  html  
    rTweedie                                html  
    random.effects                          html  
    residuals.gam                           html  
    rig                                     html  
    rmvn                                    html  
    s                                       html  
    scat                                    html  
    sdiag                                   html  
    single.index                            html  
    slanczos                                html  
    smooth.construct                        html  
    smooth.construct.ad.smooth.spec         html  
    smooth.construct.bs.smooth.spec         html  
    smooth.construct.cr.smooth.spec         html  
    smooth.construct.ds.smooth.spec         html  
    smooth.construct.fs.smooth.spec         html  
    smooth.construct.gp.smooth.spec         html  
    smooth.construct.mrf.smooth.spec        html  
    smooth.construct.ps.smooth.spec         html  
    smooth.construct.re.smooth.spec         html  
    smooth.construct.so.smooth.spec         html  
    smooth.construct.sos.smooth.spec        html  
    smooth.construct.t2.smooth.spec         html  
    smooth.construct.tensor.smooth.spec     html  
    smooth.construct.tp.smooth.spec         html  
    smooth.terms                            html  
    smooth2random                           html  
    smoothCon                               html  
    sp.vcov                                 html  
    spasm.construct                         html  
    step.gam                                html  
    summary.gam                             html  
    t2                                      html  
    te                                      html  
    tensor.prod.model.matrix                html  
    totalPenaltySpace                       html  
    trichol                                 html  
    trind.generator                         html  
    twlss                                   html  
    uniquecombs                             html  
    vcov.gam                                html  
    vis.gam                                 html  
    ziP                                     html  
    ziplss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/Recommended'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library/Recommended'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0'
configuring Java ...
Java interpreter : /usr/bin/java
Java version     : 10.0.2
Java home path   : /usr/lib/jvm/java-10-openjdk-10.0.2.13-8.el7_a32.arm
Java compiler    : not present
Java headers gen.: 
Java archive tool: 
trying to compile and link a JNI program 
detected JNI cpp flags    : 
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
make[2]: Entering directory `/tmp/Rjavareconf.1a0n3k'
gcc -std=gnu99 -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG   -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
 #include <jni.h>
                 ^
compilation terminated.
make[2]: Leaving directory `/tmp/Rjavareconf.1a0n3k'
make[2]: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME        : /usr/lib/jvm/java-10-openjdk-10.0.2.13-8.el7_a32.arm
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /builddir/build/BUILD/R-3.6.0
Done.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0'
+ cd src/nmath/standalone
+ make
(cd ../../include; make Rmath.h)
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include'
Copying source files
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
making std_unif.d from std_unif.c
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mlutils.c -o mlutils.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c d1mach.c -o d1mach.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c i1mach.c -o i1mach.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmax2.c -o fmax2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmin2.c -o fmin2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fprec.c -o fprec.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fround.c -o fround.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ftrunc.c -o ftrunc.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sign.c -o sign.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fsign.c -o fsign.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imax2.c -o imax2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imin2.c -o imin2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chebyshev.c -o chebyshev.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c log1p.c -o log1p.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgammacor.c -o lgammacor.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gammalims.c -o gammalims.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stirlerr.c -o stirlerr.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bd0.c -o bd0.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma.c -o gamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgamma.c -o lgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c beta.c -o beta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lbeta.c -o lbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c polygamma.c -o polygamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cospi.c -o cospi.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_i.c -o bessel_i.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_j.c -o bessel_j.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_k.c -o bessel_k.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_y.c -o bessel_y.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c choose.c -o choose.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c snorm.c -o snorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sexp.c -o sexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgamma.c -o dgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgamma.c -o pgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgamma.c -o qgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgamma.c -o rgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbeta.c -o dbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbeta.c -o pbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbeta.c -o qbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbeta.c -o rbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dunif.c -o dunif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c punif.c -o punif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qunif.c -o qunif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c runif.c -o runif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnorm.c -o dnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnorm.c -o pnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnorm.c -o rnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlnorm.c -o dlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plnorm.c -o plnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlnorm.c -o qlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlnorm.c -o rlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c df.c -o df.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pf.c -o pf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qf.c -o qf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rf.c -o rf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnf.c -o dnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dt.c -o dt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pt.c -o pt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qt.c -o qt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rt.c -o rt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnt.c -o dnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dchisq.c -o dchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pchisq.c -o pchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qchisq.c -o qchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rchisq.c -o rchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnchisq.c -o rnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbinom.c -o dbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbinom.c -o pbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbinom.c -o qbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbinom.c -o rbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rmultinom.c -o rmultinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dcauchy.c -o dcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pcauchy.c -o pcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qcauchy.c -o qcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rcauchy.c -o rcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dexp.c -o dexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pexp.c -o pexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qexp.c -o qexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rexp.c -o rexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgeom.c -o dgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgeom.c -o pgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgeom.c -o qgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgeom.c -o rgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dhyper.c -o dhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c phyper.c -o phyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qhyper.c -o qhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rhyper.c -o rhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbinom.c -o dnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbinom.c -o pnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbinom.c -o qnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnbinom.c -o rnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dpois.c -o dpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ppois.c -o ppois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qpois.c -o qpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpois.c -o rpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dweibull.c -o dweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pweibull.c -o pweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qweibull.c -o qweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rweibull.c -o rweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlogis.c -o dlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plogis.c -o plogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlogis.c -o qlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlogis.c -o rlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnchisq.c -o dnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnchisq.c -o pnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnchisq.c -o qnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbeta.c -o dnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbeta.c -o pnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbeta.c -o qnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnf.c -o pnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnt.c -o pnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnf.c -o qnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnt.c -o qnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ptukey.c -o ptukey.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qtukey.c -o qtukey.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c toms708.c -o toms708.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c wilcox.c -o wilcox.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c signrank.c -o signrank.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c std_unif.c -o std_unif.o
ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o
ranlib libRmath.a
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c mlutils.c -o mlutils.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c d1mach.c -o d1mach.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c i1mach.c -o i1mach.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmax2.c -o fmax2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fmin2.c -o fmin2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fprec.c -o fprec.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fround.c -o fround.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ftrunc.c -o ftrunc.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sign.c -o sign.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c fsign.c -o fsign.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imax2.c -o imax2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c imin2.c -o imin2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c chebyshev.c -o chebyshev.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c log1p.c -o log1p.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgammacor.c -o lgammacor.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gammalims.c -o gammalims.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c stirlerr.c -o stirlerr.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bd0.c -o bd0.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma.c -o gamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lgamma.c -o lgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c gamma_cody.c -o gamma_cody.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c beta.c -o beta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c lbeta.c -o lbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c polygamma.c -o polygamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c cospi.c -o cospi.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_i.c -o bessel_i.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_j.c -o bessel_j.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_k.c -o bessel_k.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c bessel_y.c -o bessel_y.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c choose.c -o choose.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c snorm.c -o snorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c sexp.c -o sexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgamma.c -o dgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgamma.c -o pgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgamma.c -o qgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgamma.c -o rgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbeta.c -o dbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbeta.c -o pbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbeta.c -o qbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbeta.c -o rbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dunif.c -o dunif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c punif.c -o punif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qunif.c -o qunif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c runif.c -o runif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnorm.c -o dnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnorm.c -o pnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnorm.c -o qnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnorm.c -o rnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlnorm.c -o dlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plnorm.c -o plnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlnorm.c -o qlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlnorm.c -o rlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c df.c -o df.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pf.c -o pf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qf.c -o qf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rf.c -o rf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnf.c -o dnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dt.c -o dt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pt.c -o pt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qt.c -o qt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rt.c -o rt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnt.c -o dnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dchisq.c -o dchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pchisq.c -o pchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qchisq.c -o qchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rchisq.c -o rchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnchisq.c -o rnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dbinom.c -o dbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pbinom.c -o pbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qbinom.c -o qbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rbinom.c -o rbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rmultinom.c -o rmultinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dcauchy.c -o dcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pcauchy.c -o pcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qcauchy.c -o qcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rcauchy.c -o rcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dexp.c -o dexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pexp.c -o pexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qexp.c -o qexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rexp.c -o rexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dgeom.c -o dgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pgeom.c -o pgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qgeom.c -o qgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rgeom.c -o rgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dhyper.c -o dhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c phyper.c -o phyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qhyper.c -o qhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rhyper.c -o rhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbinom.c -o dnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbinom.c -o pnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbinom.c -o qnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rnbinom.c -o rnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dpois.c -o dpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ppois.c -o ppois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qpois.c -o qpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rpois.c -o rpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dweibull.c -o dweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pweibull.c -o pweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qweibull.c -o qweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rweibull.c -o rweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dlogis.c -o dlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c plogis.c -o plogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qlogis.c -o qlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c rlogis.c -o rlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnchisq.c -o dnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnchisq.c -o pnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnchisq.c -o qnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c dnbeta.c -o dnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnbeta.c -o pnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnbeta.c -o qnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnf.c -o pnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c pnt.c -o pnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnf.c -o qnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qnt.c -o qnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c ptukey.c -o ptukey.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c qtukey.c -o qtukey.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c toms708.c -o toms708.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c wilcox.c -o wilcox.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c signrank.c -o signrank.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -c std_unif.c -o std_unif.lo
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libRmath.so  mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath/standalone'
+ make pdf
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
creating doc/manual/version.tex
collecting LaTeX docs for package 'base' ...
Converting parsed Rd's to LaTeX ...........................................
collecting LaTeX docs for package 'tools' ...
Converting parsed Rd's to LaTeX ......
collecting LaTeX docs for package 'utils' ...
Converting parsed Rd's to LaTeX ...............
collecting LaTeX docs for package 'grDevices' ...
Converting parsed Rd's to LaTeX .......
collecting LaTeX docs for package 'graphics' ...
Converting parsed Rd's to LaTeX .......
collecting LaTeX docs for package 'stats' ...
Converting parsed Rd's to LaTeX ..............................
collecting LaTeX docs for package 'datasets' ...
Converting parsed Rd's to LaTeX ........
collecting LaTeX docs for package 'methods' ...
Converting parsed Rd's to LaTeX ........
collecting LaTeX docs for package 'grid' ...
Converting parsed Rd's to LaTeX .........
collecting LaTeX docs for package 'splines' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'stats4' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'tcltk' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'compiler' ...
Converting parsed Rd's to LaTeX 
collecting LaTeX docs for package 'parallel' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'MASS' ...
Converting parsed Rd's to LaTeX ...............
collecting LaTeX docs for package 'lattice' ...
Converting parsed Rd's to LaTeX ......
collecting LaTeX docs for package 'Matrix' ...
Converting parsed Rd's to LaTeX ...........
collecting LaTeX docs for package 'nlme' ...
Converting parsed Rd's to LaTeX ............................
collecting LaTeX docs for package 'survival' ...
Converting parsed Rd's to LaTeX ...........
collecting LaTeX docs for package 'boot' ...
Converting parsed Rd's to LaTeX ........
collecting LaTeX docs for package 'cluster' ...
Converting parsed Rd's to LaTeX .....
collecting LaTeX docs for package 'codetools' ...
Converting parsed Rd's to LaTeX 
collecting LaTeX docs for package 'foreign' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'KernSmooth' ...
Converting parsed Rd's to LaTeX 
collecting LaTeX docs for package 'rpart' ...
Converting parsed Rd's to LaTeX ..
collecting LaTeX docs for package 'class' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'nnet' ...
Converting parsed Rd's to LaTeX 
collecting LaTeX docs for package 'spatial' ...
Converting parsed Rd's to LaTeX ..
collecting LaTeX docs for package 'mgcv' ...
Converting parsed Rd's to LaTeX ..............
PDF/LaTeX documentation: full reference index ...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo
aded.
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.
) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
No file fullrefman.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texliv
e/texmf/fonts/map/pdftex/updmap/pdftex.map}] [1] [2] [1] [2] (./base-pkg.tex
Chapter 1.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4]
Underfull \hbox (badness 6741) in paragraph at lines 135--141
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 .
Underfull \hbox (badness 4805) in paragraph at lines 135--141
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10
 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is
Underfull \hbox (badness 4316) in paragraph at lines 135--141
\T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-
wise, it is \T1/pcr/m/n/10 (double.base ^
Underfull \hbox (badness 5050) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It
Underfull \hbox (badness 1028) in paragraph at lines 141--149
\T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/pcr/m/n/10 double.base
Underfull \hbox (badness 2980) in paragraph at lines 141--149
\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 141--149
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As
Underfull \hbox (badness 1668) in paragraph at lines 152--159
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5] [6] [7]
Underfull \hbox (badness 10000) in paragraph at lines 339--342
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8] [9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 534--540
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13]
[14] [15]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
Underfull \hbox (badness 1838) in paragraph at lines 1178--1181
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[21] [22] [23] [24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670
 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
Underfull \hbox (badness 1303) in paragraph at lines 1698--1701
[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[28] [29]
Underfull \hbox (badness 10000) in paragraph at lines 1816--1818
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[30] [31]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
Underfull \hbox (badness 10000) in paragraph at lines 1991--1993
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[32] [33] [34] [35]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[38]
Underfull \hbox (badness 1107) in paragraph at lines 2460--2462
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326
 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327
 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334
 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335
 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012
 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
Underfull \hbox (badness 4927) in paragraph at lines 4267--4271
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 4267--4271
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
Underfull \hbox (badness 1199) in paragraph at lines 4596--4602
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
Underfull \hbox (badness 2573) in paragraph at lines 4607--4610
[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[70] [71]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4766--4766
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[72] [73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5019--5021
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5416--5424
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[82] [83] [84] [85] [86] [87] [88] [89]
Underfull \hbox (badness 1796) in paragraph at lines 5979--5987
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[90] [91] [92]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6175--6175
 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6176--6176
 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6311--6315
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
Underfull \hbox (badness 1635) in paragraph at lines 6353--6356
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6357--6360
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[95]
Underfull \hbox (badness 1308) in paragraph at lines 6388--6396
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[96] [97]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6542--6542
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6584--6586
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6732--6735
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6732--6735
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[101] [102]
Underfull \hbox (badness 1406) in paragraph at lines 6914--6920
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 6934--6936
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
Underfull \hbox (badness 1067) in paragraph at lines 6976--6983
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7168--7168
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
Underfull \hbox (badness 1231) in paragraph at lines 7293--7299
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7506
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7649--7649
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7887--7887
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
Underfull \hbox (badness 8132) in paragraph at lines 7988--7992
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7988--7992
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 8007--8017
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8007--8017
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[119]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8039--8043
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[120] [121] [122] [123] [124] [125]
Underfull \hbox (badness 1629) in paragraph at lines 8525--8537
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8525--8537
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8788
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
Underfull \hbox (badness 10000) in paragraph at lines 8972--8976
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[132] [133]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9063--9063
 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9065--9065
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9090--9090
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9091--9091
 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
Underfull \hbox (badness 5403) in paragraph at lines 9209--9211
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[136] [137] [138]
Underfull \hbox (badness 1603) in paragraph at lines 9439--9442
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10045--10050
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10100--10100
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10101--10101
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
Underfull \hbox (badness 1168) in paragraph at lines 10203--10208
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[150]
Underfull \hbox (badness 10000) in paragraph at lines 10242--10248
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10249--10252
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[151] [152]
Underfull \hbox (badness 2828) in paragraph at lines 10408--10412
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10408--10412
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10441--10441
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10514--10514
 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[155] [156]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10658--10658
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
Underfull \hbox (badness 6396) in paragraph at lines 10847--10855
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
Underfull \hbox (badness 10000) in paragraph at lines 10856--10858
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11073--11076
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[163] [164] [165] [166] [167] [168] [169] [170] [171]
Underfull \hbox (badness 5288) in paragraph at lines 11771--11773
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
Underfull \hbox (badness 3039) in paragraph at lines 11781--11786
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 10000) in paragraph at lines 11841--11843
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
Underfull \hbox (badness 4569) in paragraph at lines 11963--11967
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 11963--11967
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12078--12080
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12919--12919
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 2221) in paragraph at lines 13365--13374
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13365--13374
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13626--13628
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
Underfull \hbox (badness 2573) in paragraph at lines 13741--13743
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13891--13893
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14004
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14011--14014
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 14032--14032
 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 14055--14055
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
Underfull \hbox (badness 10000) in paragraph at lines 14147--14150
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14157--14157
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
Underfull \hbox (badness 10000) in paragraph at lines 14223--14226
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14240--14240
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 1472) in paragraph at lines 14293--14300
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14293--14300
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14301--14305
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[208] [209] [210]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14464--14464
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14465--14465
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14695--14695
 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 14698--14698
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
Underfull \hbox (badness 1168) in paragraph at lines 14782--14786
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14782--14786
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
Underfull \hbox (badness 6944) in paragraph at lines 14880--14883
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[216]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14905--14905
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
Underfull \hbox (badness 10000) in paragraph at lines 15043--15045
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15063--15063
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15069--15069
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
Underfull \hbox (badness 2790) in paragraph at lines 15076--15079
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 1024) in paragraph at lines 15107--15111
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[220]
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
[]\T1/ptm/m/n/10 The im-ple-men-ta-tion has \T1/pcr/m/n/10 formatC() \T1/ptm/m/
n/10 call-ing \T1/pcr/m/n/10 prettyNum()
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
\T1/ptm/m/n/10 (only if \T1/pcr/m/n/10 zero.print \T1/ptm/m/n/10 is not \T1/pcr
/m/n/10 NULL\T1/ptm/m/n/10 ) which it-self calls
Underfull \hbox (badness 2818) in paragraph at lines 15192--15194
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15203--15211
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[221] [222]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15304--15304
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15326--15326
 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16143--16143
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[235] [236]
Underfull \hbox (badness 2418) in paragraph at lines 16252--16256
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16259--16262
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16294--16301
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[237] [238] [239] [240]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16540--16540
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16565--16572
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[241] [242] [243] [244]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16834--16834
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16863--16863
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [245]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16914--16914
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[246] [247] [248] [249] [250]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17279--17279
 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[251] [252] [253] [254]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17533--17533
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257]
Underfull \hbox (badness 2435) in paragraph at lines 17796--17798
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[258]
Underfull \hbox (badness 2285) in paragraph at lines 17862--17864
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17870--17870
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[259]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17880--17880
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 17900--17900
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 18040--18040
 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18043--18043
 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18049--18049
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[262] [263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 18176--18176
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18184--18184
 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[264] [265] [266]
Underfull \hbox (badness 10000) in paragraph at lines 18389--18391
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[267]
Underfull \hbox (badness 4217) in paragraph at lines 18473--18482
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18488--18504
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[268] [269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18907--18910
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[275] [276]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19030--19030
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19165--19167
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 19214--19214
 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19215--19215
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1975) in paragraph at lines 19793--19796
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[288] [289] [290] [291] [292] [293]
Underfull \hbox (badness 1077) in paragraph at lines 20188--20193
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[294]
Underfull \hbox (badness 10000) in paragraph at lines 20202--20209
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20276--20280
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20425--20429
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 20425--20429
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20430--20437
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
[298] [299]
Underfull \hbox (badness 10000) in paragraph at lines 20561--20568
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[300]
Underfull \hbox (badness 10000) in paragraph at lines 20682--20686
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[301]
Underfull \hbox (badness 5161) in paragraph at lines 20752--20757
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[302] [303] [304]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20919--20919
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20923--20923
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[305]
Underfull \hbox (badness 3343) in paragraph at lines 20979--20983
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[306]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21065--21065
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21076--21076
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[307] [308]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21187--21187
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21190--21190
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
Underfull \hbox (badness 6380) in paragraph at lines 21235--21240
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[309] [310]
Underfull \hbox (badness 2564) in paragraph at lines 21326--21329
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21356--21356
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[311] [312]
Underfull \hbox (badness 1400) in paragraph at lines 21524--21528
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[313] [314] [315]
Underfull \hbox (badness 2469) in paragraph at lines 21694--21700
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
Underfull \hbox (badness 4531) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[316] [317] [318] [319] [320] [321] [322] [323] [324]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22321--22321
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22322--22322
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 22325--22325
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[325] [326]
Underfull \hbox (badness 1655) in paragraph at lines 22449--22453
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[327] [328] [329] [330]
Underfull \hbox (badness 2277) in paragraph at lines 22698--22701
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[331] [332] [333] [334] [335] [336] [337] [338]
Underfull \hbox (badness 1484) in paragraph at lines 23263--23271
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 23263--23271
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[339] [340]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23340--23340
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[341] [342] [343] [344] [345] [346] [347]
Underfull \hbox (badness 1448) in paragraph at lines 23845--23853
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[348] [349]
Underfull \hbox (badness 3849) in paragraph at lines 23959--23964
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[350]
Underfull \hbox (badness 7308) in paragraph at lines 24036--24042
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 10000) in paragraph at lines 24036--24042
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 1210) in paragraph at lines 24036--24042
[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[351] [352]
Underfull \hbox (badness 10000) in paragraph at lines 24199--24201
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[353] [354] [355]
Underfull \hbox (badness 6188) in paragraph at lines 24418--24421
[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 2197) in paragraph at lines 24902--24906
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24902--24906
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[363]
Underfull \hbox (badness 2846) in paragraph at lines 24916--24920
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
Underfull \hbox (badness 1990) in paragraph at lines 24916--24920
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24958--24958
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24962--24962
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[364]
Underfull \hbox (badness 10000) in paragraph at lines 25010--25016
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25010--25016
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 25023--25025
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25074--25074
 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[366] [367] [368]
Underfull \hbox (badness 8189) in paragraph at lines 25267--25273
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[369] [370] [371]
Underfull \hbox (badness 1694) in paragraph at lines 25489--25492
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[372] [373] [374]
Underfull \hbox (badness 1603) in paragraph at lines 25736--25738
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[375] [376]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25863--25871
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[377] [378]
Underfull \hbox (badness 3271) in paragraph at lines 26070--26073
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[379] [380] [381]
Underfull \hbox (badness 3138) in paragraph at lines 26370--26376
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[382]
Underfull \hbox (badness 1194) in paragraph at lines 26383--26386
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 1389) in paragraph at lines 26409--26411
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 26429--26435
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26444--26449
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Underfull \hbox (badness 1009) in paragraph at lines 26462--26465
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[383]
Underfull \hbox (badness 10000) in paragraph at lines 26478--26481
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 26500--26507
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[384] [385] [386] [387]
Underfull \vbox (badness 10000) has occurred while \output is active [388]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26844--26844
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[389] [390]
Underfull \hbox (badness 10000) in paragraph at lines 27004--27007
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
Underfull \hbox (badness 1062) in paragraph at lines 27004--27007
\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[391] [392] [393]
Underfull \hbox (badness 10000) in paragraph at lines 27273--27279
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 27273--27279
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
[394]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27295--27295
 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27307--27307
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[395] [396] [397] [398] [399] [400] [401]
Underfull \hbox (badness 1817) in paragraph at lines 27741--27745
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[402]
Underfull \hbox (badness 1796) in paragraph at lines 27809--27812
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[403] [404] [405]
Underfull \hbox (badness 10000) in paragraph at lines 28009--28012
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[406] [407] [408] [409] [410] [411] [412] [413] [414] [415]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28686--28686
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[416] [417] [418] [419]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28952--28952
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28963--28963
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28969--28969
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28970--28970
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28973--28973
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[420]
Underfull \hbox (badness 7415) in paragraph at lines 29048--29052
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[421]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29069--29069
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 29115--29115
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[422] [423]
Underfull \hbox (badness 3713) in paragraph at lines 29238--29249
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[424]
Underfull \hbox (badness 1248) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
Underfull \hbox (badness 10000) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[425] [426]
Underfull \hbox (badness 1533) in paragraph at lines 29500--29503
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[427] [428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29645--29645
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29663--29674
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[430] [431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29807--29807
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29809--29809
 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29810--29810
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29811--29811
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29812--29812
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29819--29819
 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[432] [433] [434] [435] [436] [437]
Underfull \hbox (badness 4048) in paragraph at lines 30166--30171
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
Underfull \hbox (badness 1824) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[438] [439] [440] [441] [442] [443] [444] [445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30707--30707
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 7558) in paragraph at lines 31209--31213
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31219--31221
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
[452]
Underfull \hbox (badness 5417) in paragraph at lines 31224--31227
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31228--31230
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31231--31233
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31636--31640
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31980--31980
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31983--31983
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32367--32367
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[470] [471] [472] [473] [474] [475]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32802--32802
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[476]
Underfull \hbox (badness 1158) in paragraph at lines 32906--32911
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[477]
Underfull \hbox (badness 10000) in paragraph at lines 32933--32939
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1762) in paragraph at lines 32933--32939
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[478] [479]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33091--33091
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[480] [481] [482]
Underfull \hbox (badness 8151) in paragraph at lines 33351--33354
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[483] [484] [485] [486]
Underfull \hbox (badness 1210) in paragraph at lines 33586--33588
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498]
[499] [500]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34523--34523
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[501] [502] [503]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34775--34775
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34777--34777
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[504]
Underfull \hbox (badness 4954) in paragraph at lines 34820--34826
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 34820--34826
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[505] [506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34931--34931
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35259--35259
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
[511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35274--35274
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[512] [513] [514] [515] [516] [517]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35715--35715
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35716--35716
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[518] [519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35980--35980
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
Underfull \hbox (badness 6110) in paragraph at lines 36064--36074
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 36064--36074
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1460) in paragraph at lines 36120--36127
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[523] [524] [525] [526]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 36397--36397
 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[527] [528] [529] [530] [531] [532] [533] [534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36959--36959
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[535] [536] [537] [538]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 37207--37207
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[539]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37251--37251
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[540] [541] [542] [543] [544] [545]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37685--37685
 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37688--37688
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[546]
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[547]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37792--37792
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[548] [549] [550] [551]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38093--38093
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[552]
Underfull \vbox (badness 7777) has occurred while \output is active [553]
[554]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38258--38258
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38296--38296
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
Underfull \hbox (badness 4792) in paragraph at lines 38345--38350
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 38345--38350
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[556]
Underfull \hbox (badness 2452) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[557] [558] [559]
Underfull \hbox (badness 10000) in paragraph at lines 38623--38627
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 38638--38641
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[560] [561]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38770--38770
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[562]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38840--38840
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[563] [564] [565]
Underfull \hbox (badness 1082) in paragraph at lines 38984--38987
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[566] [567]
Underfull \hbox (badness 1038) in paragraph at lines 39175--39178
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[568] [569] [570] [571] [572] [573]
Underfull \hbox (badness 1442) in paragraph at lines 39538--39542
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[574] [575] [576]
Underfull \hbox (badness 4096) in paragraph at lines 39784--39787
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[577] [578]
Underfull \hbox (badness 7888) in paragraph at lines 39898--39902
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[579] [580]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40052--40052
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40054--40054
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
[581]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40056--40056
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 40069--40071
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[582]
Underfull \hbox (badness 10000) in paragraph at lines 40149--40152
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[583] [584]
Underfull \hbox (badness 3872) in paragraph at lines 40267--40270
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[585]
Underfull \hbox (badness 5475) in paragraph at lines 40333--40337
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 10000) in paragraph at lines 40751--40758
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40807--40816
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40807--40816
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 2503) in paragraph at lines 40817--40825
\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[592]
Underfull \hbox (badness 1337) in paragraph at lines 40883--40891
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40892--40895
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[593]
Underfull \hbox (badness 3460) in paragraph at lines 40946--40949
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 40950--40952
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40959--40959
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[594] [595] [596]
Underfull \hbox (badness 10000) in paragraph at lines 41176--41178
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[597] [598]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41298--41298
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41300--41300
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [599]
[600] [601] [602] [603]
Underfull \hbox (badness 6542) in paragraph at lines 41662--41664
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[604] [605]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41781--41781
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[606]
Underfull \hbox (badness 1708) in paragraph at lines 41849--41857
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 41849--41857
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 4859) in paragraph at lines 41879--41884
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[607]
Underfull \hbox (badness 3895) in paragraph at lines 41941--41953
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 41941--41953
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[608] [609] [610] [611] [612]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 42264--42264
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[613] [614] [615] [616] [617] [618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42731--42731
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[619]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42740--42740
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[620]
Underfull \hbox (badness 1803) in paragraph at lines 42865--42868
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
[621]
Underfull \hbox (badness 3471) in paragraph at lines 42869--42876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[622] [623] [624]
Underfull \hbox (badness 3668) in paragraph at lines 43084--43086
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[625]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 43188--43188
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[626]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43263--43263
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 43271--43271
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[627] [628]
Underfull \hbox (badness 6220) in paragraph at lines 43401--43406
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 43401--43406
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
[629]
Underfull \hbox (badness 10000) in paragraph at lines 43422--43427
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
Underfull \hbox (badness 4229) in paragraph at lines 43422--43427
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[630]
Underfull \hbox (badness 2818) in paragraph at lines 43512--43518
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[631]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 43547--43547
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[632]
Underfull \hbox (badness 1622) in paragraph at lines 43641--43643
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[633] [634] [635] [636] [637]
Underfull \hbox (badness 2846) in paragraph at lines 44004--44008
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44044--44044
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
Underfull \hbox (badness 3209) in paragraph at lines 44065--44069
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[639]) (./compiler-pkg.tex [640]
Chapter 2.
[641]
Underfull \hbox (badness 2884) in paragraph at lines 105--119
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 105--119
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
Underfull \vbox (badness 1033) has occurred while \output is active [651]
[652] [653] [654] [655]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 702--705
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[660] [661]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1146--1149
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1544
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1541--1544
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[669] [670] [671]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1730--1733
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681] [682] [683] [684] [685] [686]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[688]
Underfull \vbox (badness 1789) has occurred while \output is active [689]
[690]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[691] [692]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[704]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
Underfull \hbox (badness 10000) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[725] [726]
Underfull \hbox (badness 10000) in paragraph at lines 379--387
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
Underfull \hbox (badness 1748) in paragraph at lines 379--387
\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[727] [728]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[738] [739]
Underfull \hbox (badness 10000) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
Underfull \hbox (badness 1173) in paragraph at lines 1322--1325
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[741] [742] [743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1565) in paragraph at lines 1810--1815
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1810--1815
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[749]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
Underfull \hbox (badness 1184) in paragraph at lines 1934--1944
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 1934--1944
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[750] [751]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[752] [753]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
Underfull \hbox (badness 2326) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
Underfull \hbox (badness 2318) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
Underfull \hbox (badness 2460) in paragraph at lines 2341--2351
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
Underfull \hbox (badness 1221) in paragraph at lines 2341--2351
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[756] [757]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
Underfull \vbox (badness 10000) has occurred while \output is active [758]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560
 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561
 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829
Underfull \vbox (badness 10000) has occurred while \output is active [764]
[765] [766] [767] [768]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161
 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3246--3246
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
Underfull \hbox (badness 1264) in paragraph at lines 3384--3389
\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[772] [773] [774]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545
 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
Underfull \hbox (badness 8170) in paragraph at lines 3571--3574
[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[775]
Underfull \hbox (badness 10000) in paragraph at lines 3655--3659
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space&
oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
Underfull \hbox (badness 5260) in paragraph at lines 3785--3788
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
Underfull \hbox (badness 5939) in paragraph at lines 4113--4118
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
Underfull \hbox (badness 3612) in paragraph at lines 4514--4519
\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
Underfull \hbox (badness 1348) in paragraph at lines 4828--4831
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[793]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
Underfull \hbox (badness 7522) in paragraph at lines 4892--4898
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[794]
Underfull \hbox (badness 1112) in paragraph at lines 4923--4927
[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[795]
Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[796] [797] [798]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
Underfull \hbox (badness 7397) in paragraph at lines 5256--5260
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[799] [800]
Underfull \hbox (badness 1552) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5390--5392
[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5422--5428
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[801]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[802] [803]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
Underfull \hbox (badness 10000) in paragraph at lines 5747--5749
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[807] [808] [809] [810] [811]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458
 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465
 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 6728--6733
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1803) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[822]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833
 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
Underfull \hbox (badness 5954) in paragraph at lines 6872--6875
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https :
[824]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
Underfull \hbox (badness 10000) in paragraph at lines 7084--7091
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7084--7091
\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[827]
Underfull \hbox (badness 5607) in paragraph at lines 7168--7172
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
Underfull \hbox (badness 5637) in paragraph at lines 7345--7351
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
[830]
Underfull \hbox (badness 1721) in paragraph at lines 7378--7381
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[831] [832]
Underfull \hbox (badness 1231) in paragraph at lines 7546--7548
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.
Underfull \hbox (badness 4647) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[837] [838] [839]
Underfull \hbox (badness 3792) in paragraph at lines 177--180
[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[840]
Underfull \hbox (badness 1412) in paragraph at lines 287--292
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[844] [845]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846] [847]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 694--698
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[848]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[849]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818
 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[850] [851]
Underfull \hbox (badness 10000) in paragraph at lines 960--964
[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977
 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979
 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855] [856] [857] [858]
Underfull \hbox (badness 1024) in paragraph at lines 1425--1433
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1459--1461
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1530--1530
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1536--1536
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1537--1537
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
Underfull \hbox (badness 10000) in paragraph at lines 1837--1843
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[865]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1874--1874
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1883--1883
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1968--1968
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2097--2097
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2102--2102
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2376--2376
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
Underfull \hbox (badness 1009) in paragraph at lines 2388--2395
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[874]
Underfull \hbox (badness 7273) in paragraph at lines 2470--2474
[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2483--2483
 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
Underfull \hbox (badness 1226) in paragraph at lines 2878--2882
\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2931--2931
 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[882]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2935--2935
 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
Underfull \hbox (badness 10000) in paragraph at lines 2987--2990
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[883] [884] [885]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3192--3192
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3197--3197
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3522--3522
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3541--3541
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[891]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3545--3545
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[892] [893]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3722--3722
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3723--3723
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3762--3762
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [895]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3814--3814
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3822--3822
 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3832--3832
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
Underfull \hbox (badness 10000) in paragraph at lines 3895--3899
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[897] [898]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4006--4006
 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[899] [900] [901]
Underfull \hbox (badness 3930) in paragraph at lines 4213--4215
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[902] [903] [904] [905] [906]
Underfull \hbox (badness 1286) in paragraph at lines 4524--4527
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[907]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4629--4629
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4634--4634
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[908]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4678--4678
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
Underfull \hbox (badness 1264) in paragraph at lines 4752--4765
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[910] [911]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4895
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[912]
Underfull \hbox (badness 10000) in paragraph at lines 5020--5023
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf, id=1586
6, 289.08pt x 289.08pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf>
[913 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 5081--5083
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf, id=1588
0, 259.97125pt x 332.24126pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [914]
[915 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/oma.pdf>]
[916]
Underfull \hbox (badness 10000) in paragraph at lines 5271--5273
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[917]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5327--5327
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5328--5328
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5693--5693
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5694--5694
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
Underfull \hbox (badness 1360) in paragraph at lines 5745--5749
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[924] [925] [926] [927] [928] [929] [930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6179--6179
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6185--6185
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
Underfull \hbox (badness 10000) in paragraph at lines 6612--6614
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
Underfull \hbox (badness 1028) in paragraph at lines 6706--6708
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf, id=1632
3, 361.35pt x 50.1875pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750
[][] 
[939 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6843--6843
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6874--6874
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [941]
[942]
Underfull \hbox (badness 10000) in paragraph at lines 6996--6998
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7023--7023
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7029--7029
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
Underfull \hbox (badness 2600) in paragraph at lines 7089--7091
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[944] [945] [946] [947]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7321--7321
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7708--7708
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7712--7712
 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7724--7724
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[955] [956] [957] [958] [959]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8073--8073
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8076--8076
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8080--8080
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8251--8251
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8252--8252
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[963] [964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8356--8356
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
Underfull \hbox (badness 2080) in paragraph at lines 8367--8372
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[965]
Underfull \hbox (badness 1112) in paragraph at lines 8415--8419
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[966]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8475--8475
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8490--8490
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8621--8621
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8806--8806
 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[971]
Underfull \hbox (badness 10000) in paragraph at lines 8834--8836
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
Underfull \hbox (badness 1584) in paragraph at lines 8868--8874
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8916 \HeaderA{units}{Graphical Units}{units}
                                               [973]
Underfull \hbox (badness 1205) in paragraph at lines 8981--8983
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 9100--9100
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
Underfull \hbox (badness 10000) in paragraph at lines 476--482
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
Underfull \hbox (badness 1024) in paragraph at lines 476--482
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[985] [986] [987] [988] [989] [990] [991] [992] [993] [994]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
Underfull \hbox (badness 1430) in paragraph at lines 1166--1171
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[995] [996] [997] [998]
Underfull \hbox (badness 3219) in paragraph at lines 1380--1383
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[999] [1000] [1001] [1002] [1003] [1004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1982--1982
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1983--1983
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
Underfull \hbox (badness 2961) in paragraph at lines 2018--2023
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1009]
Underfull \hbox (badness 1430) in paragraph at lines 2077--2082
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
Underfull \hbox (badness 4479) in paragraph at lines 2106--2109
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[1010] [1011] [1012]
Underfull \hbox (badness 2894) in paragraph at lines 2313--2320
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[1013] [1014] [1015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
Underfull \hbox (badness 1430) in paragraph at lines 2481--2486
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1016]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540
 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
[1019]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1020] [1021] [1022]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1023] [1024] [1025] [1026] [1027]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028] [1029]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
Underfull \hbox (badness 2799) in paragraph at lines 3411--3417
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1030] [1031]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1035]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747
 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046]
[1047]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1048]
Underfull \hbox (badness 1430) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1049] [1050] [1051]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061]
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
Underfull \hbox (badness 6859) in paragraph at lines 6056--6062
[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
Underfull \hbox (badness 10000) in paragraph at lines 6056--6062
\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1072] [1073] [1074] [1075] [1076]
Underfull \hbox (badness 1867) in paragraph at lines 6366--6368
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1077]
Underfull \hbox (badness 10000) in paragraph at lines 6403--6409
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1078] [1079]
Underfull \hbox (badness 1371) in paragraph at lines 6535--6538
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
[1080] [1081] [1082]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1087] [1088] [1089]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1090] [1091]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558
 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568
 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619
 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1093]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637
 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640
 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657
 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672
 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
Underfull \vbox (badness 10000) has occurred while \output is active [1094]
[1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105]
[1106] [1107] [1108]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1111] [1112] [1113]
Underfull \hbox (badness 1478) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
[1114] [1115]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360
 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
Underfull \hbox (badness 1194) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1119]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
Underfull \hbox (badness 10000) in paragraph at lines 3403--3408
[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
Underfull \hbox (badness 6268) in paragraph at lines 3403--3408
\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1130] [1131]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1132]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651
[]
[1133] [1134]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
Underfull \hbox (badness 10000) in paragraph at lines 3809--3810
[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
Underfull \hbox (badness 10000) in paragraph at lines 3846--3847
[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
Underfull \hbox (badness 6157) in paragraph at lines 3908--3912
[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1136] [1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 4135--4137
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
Underfull \hbox (badness 2126) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1146] [1147] [1148]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1149] [1150] [1151] [1152]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1154]
[1155]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1161] [1162] [1163] [1164] [1165] [1166]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1167] [1168]
Underfull \hbox (badness 1248) in paragraph at lines 6343--6347
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6343--6347
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1169]
Underfull \hbox (badness 4647) in paragraph at lines 6498--6500
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1172]
Underfull \vbox (badness 10000) has occurred while \output is active [1173]
[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009
 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204
 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1180]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1181] [1182]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1183] [1184]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1196]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1208] [1209] [1210] [1211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1227]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1228] [1229]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1230] [1231] [1232]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 744--753
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1237] [1238]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030
 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
Underfull \hbox (badness 5388) in paragraph at lines 1145--1150
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1243]
Underfull \hbox (badness 10000) in paragraph at lines 1169--1177
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1244] [1245]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1411--1413
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1247] [1248]) (./splines-pkg.tex
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94
 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1269]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2724--2724
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2964--2964
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3173--3175
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3221--3221
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3222--3222
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3613--3613
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3891--3891
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4180--4180
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4181--4181
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4419--4419
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
Underfull \hbox (badness 3989) in paragraph at lines 4679--4686
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1332] [1333] [1334] [1335] [1336] [1337]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5064--5064
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5066--5066
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1338] [1339] [1340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5287--5287
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5305--5305
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5332--5334
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5515--5520
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5713--5713
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5880--5880
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6065--6065
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
Underfull \hbox (badness 10000) in paragraph at lines 6240--6245
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1355] [1356] [1357] [1358]
Underfull \hbox (badness 5954) in paragraph at lines 6436--6438
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
Underfull \hbox (badness 2503) in paragraph at lines 6518--6521
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6522--6524
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6525--6530
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
Underfull \hbox (badness 7238) in paragraph at lines 6561--6564
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6596--6596
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6611--6611
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1361]
[1362] [1363] [1364]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6870--6870
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7268--7272
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7367--7370
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7507
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
Underfull \hbox (badness 10000) in paragraph at lines 7914--7919
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 1210) in paragraph at lines 8269--8271
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8732--8732
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1393]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8777--8777
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8780--8780
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8918--8918
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9345--9345
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9346--9346
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9525--9527
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9986--9992
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10199--10202
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10435--10435
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10461--10466
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
Underfull \hbox (badness 4132) in paragraph at lines 10500--10504
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10554--10560
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10605--10608
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10821--10824
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10902--10906
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
Underfull \hbox (badness 10000) in paragraph at lines 10944--10950
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10982--10987
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11115--11118
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11298--11301
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11399--11399
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11432--11432
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
Underfull \hbox (badness 10000) in paragraph at lines 11445--11449
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11625--11628
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11764--11764
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11779 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11832--11832
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11844--11844
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 11897--11902
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11914--11916
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12257--12257
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12507--12509
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12530--12532
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12599--12601
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12837--12839
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12843--12847
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12843--12847
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13550--13550
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13593--13598
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13796
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1468] [1469] [1470] [1471] [1472]
Underfull \hbox (badness 1163) in paragraph at lines 14125--14133
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14245--14250
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14431--14431
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14432--14432
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14775--14775
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14776--14776
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14869--14869
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15275--15278
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15369--15369
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15994--15994
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16132--16137
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1503]
Underfull \hbox (badness 1648) in paragraph at lines 16198--16200
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16283--16283
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16841--16841
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17069--17069
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17827--17827
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17987--17987
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18081--18081
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18572--18575
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18585--18589
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18593--18597
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1541]
Underfull \hbox (badness 2042) in paragraph at lines 18651--18653
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1542]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18757--18757
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1543]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18800--18800
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18818--18818
 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 18821--18821
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18841--18841
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1544]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18844--18844
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 18879--18890
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 18879--18890
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18942--18942
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1546] [1547] [1548]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19167--19167
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1549]
Underfull \hbox (badness 1337) in paragraph at lines 19243--19246
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1550] [1551] [1552] [1553] [1554] [1555]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19562--19562
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1556]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19650--19650
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 19652--19652
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19654--19654
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1557]
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for
Underfull \hbox (badness 5260) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1558]
Underfull \hbox (badness 3049) in paragraph at lines 19739--19743
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1559] [1560] [1561]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19987--19987
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1562]
Underfull \hbox (badness 1194) in paragraph at lines 19997--20000
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1563]
Underfull \hbox (badness 1107) in paragraph at lines 20055--20057
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20110--20110
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1564]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20117--20117
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1565]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20211--20211
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1566] [1567]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20336--20336
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1568]
Underfull \hbox (badness 7740) in paragraph at lines 20399--20401
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1569]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20447--20447
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20539--20539
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20544--20544
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581]
[1582] [1583]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21398--21398
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1584]
Underfull \hbox (badness 6859) in paragraph at lines 21465--21472
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21476--21482
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595]
[1596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22214--22214
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1597] [1598] [1599] [1600] [1601]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22498--22498
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22499--22499
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1602] [1603] [1604] [1605] [1606]
Underfull \hbox (badness 1337) in paragraph at lines 22823--22829
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23388--23388
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1615] [1616]
Underfull \hbox (badness 1028) in paragraph at lines 23529--23532
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1617] [1618]
Underfull \hbox (badness 10000) in paragraph at lines 23639--23642
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1619]
Underfull \hbox (badness 7944) in paragraph at lines 23694--23696
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23756--23758
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1621] [1622]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23858--23858
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1623] [1624] [1625]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24078--24078
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1626] [1627]
Underfull \hbox (badness 10000) in paragraph at lines 24224--24227
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1628]
Underfull \hbox (badness 2134) in paragraph at lines 24276--24280
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24289--24289
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1629] [1630] [1631] [1632] [1633] [1634] [1635]
Underfull \hbox (badness 6268) in paragraph at lines 24753--24758
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24781--24781
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1637] [1638] [1639]
Underfull \hbox (badness 1867) in paragraph at lines 24958--24960
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25007--25007
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1641] [1642] [1643]
Underfull \hbox (badness 2495) in paragraph at lines 25197--25206
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1644]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25279--25279
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 25286--25288
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1645]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25373--25373
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25398--25398
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25401--25401
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1646] [1647] [1648]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25624--25624
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 25627--25633
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1649]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25673--25673
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25694--25694
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1650] [1651]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25798--25798
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1652]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25865--25865
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1653] [1654] [1655] [1656] [1657] [1658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26244--26244
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1659] [1660]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26425--26425
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26431--26431
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26440--26440
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26441--26441
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1662]
Underfull \hbox (badness 2922) in paragraph at lines 26510--26515
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26547--26547
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26550--26550
 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
[1663]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26559--26559
 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26560--26560
 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 26564--26564
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
Underfull \hbox (badness 3240) in paragraph at lines 26618--26621
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1664]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26639--26639
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26642--26642
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1665]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26725--26725
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26729--26729
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26739--26739
 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
[1666]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 26744--26744
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 26780--26786
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26802--26802
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1667]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26818--26818
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1668] [1669]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26932--26932
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1670]
Underfull \hbox (badness 2922) in paragraph at lines 26994--26999
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27032--27032
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1671]
Underfull \hbox (badness 2922) in paragraph at lines 27081--27086
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27112--27112
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
Underfull \hbox (badness 2922) in paragraph at lines 27146--27151
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1673]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27171--27171
 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27175--27175
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27195--27195
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27205--27205
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
[1674]
Underfull \hbox (badness 2922) in paragraph at lines 27240--27245
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27262--27262
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1675]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27280--27280
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
Underfull \hbox (badness 6493) in paragraph at lines 27332--27337
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27359--27359
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27361--27361
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27364--27364
 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27367--27367
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687]
[1688] [1689] [1690]
Underfull \hbox (badness 3396) in paragraph at lines 28291--28293
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1691] [1692] [1693]
Underfull \hbox (badness 2237) in paragraph at lines 28468--28470
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1694] [1695]
Underfull \hbox (badness 2591) in paragraph at lines 28632--28634
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1696]
Underfull \hbox (badness 2237) in paragraph at lines 28678--28681
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1697]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28751--28751
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1698] [1699]
Underfull \hbox (badness 3407) in paragraph at lines 28859--28863
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1700] [1701]
Underfull \hbox (badness 1337) in paragraph at lines 28992--28996
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1702] [1703] [1704] [1705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29240--29240
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29268--29268
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1706]
Underfull \hbox (badness 1616) in paragraph at lines 29294--29297
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1707]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 29373--29373
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1708]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29450--29450
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1709] [1710]
Underfull \hbox (badness 2205) in paragraph at lines 29539--29544
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30134--30134
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30135--30135
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1720] [1721] [1722] [1723] [1724]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30435--30435
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30436--30436
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1725] [1726]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 30562--30562
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30571--30571
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1727]
[1728] [1729]
Underfull \hbox (badness 1337) in paragraph at lines 30788--30792
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738]
Underfull \hbox (badness 1337) in paragraph at lines 31315--31319
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1739] [1740] [1741] [1742] [1743] [1744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 31742--31742
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1745]
Underfull \hbox (badness 6775) in paragraph at lines 31799--31804
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 31862--31862
 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1747]) (./stats4-pkg.tex [1748]
Chapter 11.
[1749] [1750] [1751]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1752] [1753] [1754]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1755] [1756] [1757])
(./tcltk-pkg.tex [1758]
Chapter 12.
[1759] [1760] [1761] [1762]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1763] [1764] [1765]
Underfull \vbox (badness 10000) has occurred while \output is active [1766]
Underfull \hbox (badness 1292) in paragraph at lines 664--671
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777]
Underfull \hbox (badness 1189) in paragraph at lines 1407--1410
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1778]) (./tools-pkg.tex
Chapter 13.
[1779]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1780]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via
Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1781]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1782]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1783]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1784] [1785] [1786] [1787] [1788] [1789] [1790]
Overfull \vbox (7.18602pt too high) has occurred while \output is active
[1791] [1792]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1793] [1794] [1795]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123
 []                              \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124
 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[] 
Underfull \hbox (badness 1112) in paragraph at lines 1139--1149
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
Underfull \hbox (badness 3724) in paragraph at lines 1139--1149
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1796]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1797]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
[1798] [1799]
Underfull \hbox (badness 10000) in paragraph at lines 1363--1366
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
[1800] [1801] [1802] [1803] [1804]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689
 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1805] [1806] [1807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1808] [1809] [1810]
[1811]
Underfull \hbox (badness 1142) in paragraph at lines 2168--2174
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
Overfull \hbox (101.58032pt too wide) in paragraph at lines 2202--2202
 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1812]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203
 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
Underfull \hbox (badness 2359) in paragraph at lines 2230--2237
[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
 and site spe-cific com-pi-la-
Underfull \hbox (badness 1102) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
Underfull \hbox (badness 4168) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
/n/10 with
[1813]
Underfull \hbox (badness 1342) in paragraph at lines 2282--2288
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1814]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358
 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1815]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404
 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430
 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1816] [1817] [1818] [1819]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2696--2696
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1820]
Underfull \hbox (badness 2486) in paragraph at lines 2741--2749
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1821] [1822] [1823] [1824] [1825]
Underfull \hbox (badness 1072) in paragraph at lines 3119--3121
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1826] [1827] [1828] [1829] [1830]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3455--3455
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1831] [1832] [1833] [1834]
Underfull \hbox (badness 4108) in paragraph at lines 3703--3710
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3803--3803
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3806--3806
 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
Underfull \hbox (badness 10000) in paragraph at lines 3823--3825
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
Underfull \hbox (badness 2932) in paragraph at lines 3840--3846
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1837] [1838]
Underfull \hbox (badness 7832) in paragraph at lines 3962--3965
[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1839]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4038--4038
 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1840]
Underfull \hbox (badness 1137) in paragraph at lines 4064--4066
[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1841] [1842] [1843]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4249--4249
 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1844] [1845]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
Underfull \hbox (badness 10000) in paragraph at lines 4422--4425
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1846]
Underfull \hbox (badness 6859) in paragraph at lines 4438--4443
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4446--4452
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
Underfull \hbox (badness 2941) in paragraph at lines 4446--4452
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1847] [1848] [1849]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4645--4645
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4646--4646
 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[] 
Underfull \hbox (badness 3240) in paragraph at lines 4658--4661
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 4662--4672
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4697--4703
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4697--4703
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1850]
Underfull \hbox (badness 1571) in paragraph at lines 4725--4729
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
Underfull \hbox (badness 2772) in paragraph at lines 4751--4756
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1851] [1852] [1853]) (./utils-pkg.tex [1854]
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1855] [1856] [1857] [1858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1859]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 382--384
[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1861]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448
 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450
 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467
 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1862] [1863]
Underfull \hbox (badness 1946) in paragraph at lines 624--628
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1864]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 680--680
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 717--723
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1865]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1866]
Underfull \hbox (badness 4505) in paragraph at lines 850--856
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1867] [1868] [1869]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1870]
Underfull \hbox (badness 1748) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1661) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1871]
Underfull \hbox (badness 10000) in paragraph at lines 1209--1212
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1872]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1881] [1882]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1883] [1884]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1885]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1886] [1887] [1888]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344
 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1889] [1890]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1891]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1892] [1893]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1894] [1895] [1896]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1897] [1898] [1899] [1900]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1901]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1902]
Underfull \hbox (badness 2452) in paragraph at lines 3359--3362
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1903] [1904] [1905] [1906] [1907] [1908]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1909] [1910]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3906--3914
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1911]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 3997--4002
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1912] [1913]
Underfull \hbox (badness 4660) in paragraph at lines 4119--4122
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1914] [1915] [1916]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1917]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1918]
Underfull \hbox (badness 1931) in paragraph at lines 4446--4453
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1919] [1920] [1921] [1922] [1923]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1924]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1925] [1926] [1927]
[1928] [1929] [1930] [1931] [1932]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1941]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1942]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1943] [1944] [1945]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1946]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6338--6341
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1947] [1948]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1949] [1950]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 5331) in paragraph at lines 6644--6650
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
[1951]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
[1952]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1953]
Underfull \hbox (badness 1314) in paragraph at lines 6877--6884
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6934--6939
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1955]
Underfull \hbox (badness 5133) in paragraph at lines 6993--6997
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7007--7010
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1956] [1957]
Underfull \hbox (badness 4132) in paragraph at lines 7174--7176
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1958] [1959] [1960]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7341--7341
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1961] [1962]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7484--7484
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1963]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7526
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1964] [1965]
Underfull \hbox (badness 10000) in paragraph at lines 7709--7711
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1859) in paragraph at lines 7937--7940
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1970]
Underfull \hbox (badness 1655) in paragraph at lines 8030--8033
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8041--8041
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8045--8045
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8053--8053
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1971] [1972]
Underfull \hbox (badness 1917) in paragraph at lines 8132--8134
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1973] [1974] [1975] [1976]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8404--8404
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8405--8405
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
Underfull \hbox (badness 10000) in paragraph at lines 8434--8436
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 8448--8450
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8456--8461
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8502--8502
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8503--8503
 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[1978] [1979]
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8632--8637
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8639--8642
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[1980] [1981]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8755--8755
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8756--8756
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8927--8927
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1984] [1985]
Underfull \hbox (badness 1789) in paragraph at lines 9058--9060
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 5203) in paragraph at lines 9631--9634
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1994] [1995] [1996]
Underfull \hbox (badness 1394) in paragraph at lines 9857--9864
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[1997]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9881--9881
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1998] [1999]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10042--10042
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2000] [2001]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10223--10223
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[2002] [2003]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10309--10309
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10312--10312
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10317--10317
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2004]
Underfull \hbox (badness 2027) in paragraph at lines 10389--10392
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2005] [2006] [2007]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10662--10662
 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10663--10663
 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2008]
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10903--10903
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2012] [2013] [2014] [2015]
Underfull \hbox (badness 10000) in paragraph at lines 11163--11167
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2016]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11181--11181
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11186--11186
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2017] [2018]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11370--11370
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2019] [2020]
Underfull \hbox (badness 1917) in paragraph at lines 11494--11497
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11494--11497
\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2021]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11517--11517
 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2022]
Underfull \hbox (badness 10000) in paragraph at lines 11580--11582
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
Underfull \hbox (badness 6725) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
Underfull \hbox (badness 6428) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2023] [2024]
Underfull \hbox (badness 3646) in paragraph at lines 11756--11758
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2025]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 11794--11794
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2026] [2027] [2028]
Underfull \hbox (badness 10000) in paragraph at lines 11975--11979
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12006--12012
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2029] [2030]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12182--12182
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
Underfull \hbox (badness 1009) in paragraph at lines 12200--12212
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2031]
Underfull \hbox (badness 2600) in paragraph at lines 12237--12239
[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2032]
Underfull \hbox (badness 1043) in paragraph at lines 12280--12285
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2033] [2034] [2035] [2036]
Underfull \hbox (badness 1888) in paragraph at lines 12573--12576
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 12588--12591
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2037]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12629--12629
 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
Underfull \hbox (badness 2158) in paragraph at lines 12684--12687
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[2038]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12732--12732
 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2039] [2040]
Underfull \hbox (badness 2302) in paragraph at lines 12889--12891
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2041] [2042]
Underfull \hbox (badness 3333) in paragraph at lines 12996--12998
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2043] [2044] [2045]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13161--13161
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
Underfull \hbox (badness 2012) in paragraph at lines 13185--13190
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
Underfull \hbox (badness 5970) in paragraph at lines 13194--13197
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13194--13197
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2046]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13249--13249
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2047]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 13280--13280
 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13287--13287
 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13289--13289
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
[2048] [2049]
Underfull \hbox (badness 10000) in paragraph at lines 13457--13459
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[2050] [2051] [2052]
Underfull \hbox (badness 6300) in paragraph at lines 13614--13621
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[2053] [2054]
Underfull \hbox (badness 2020) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2055] [2056]
Underfull \hbox (badness 5022) in paragraph at lines 13923--13927
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2057] [2058] [2059]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14094--14094
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2060] [2061] [2062] [2063] [2064] [2065]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14534--14534
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14540--14540
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Underfull \hbox (badness 4467) in paragraph at lines 14561--14563
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 14574--14578
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 1694) in paragraph at lines 14588--14592
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
Underfull \hbox (badness 1052) in paragraph at lines 14600--14602
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2066]
Underfull \hbox (badness 10000) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
Underfull \hbox (badness 1509) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
Underfull \hbox (badness 10000) in paragraph at lines 14651--14656
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 14659--14662
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2067]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14713--14713
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2068] [2069] [2070]
Underfull \hbox (badness 10000) in paragraph at lines 14915--14918
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Underfull \hbox (badness 1253) in paragraph at lines 14915--14918
[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2071]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 14931--14931
 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14998--14998
 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 15020--15020
 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2073] [2074]
Underfull \hbox (badness 1297) in paragraph at lines 15151--15153
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2075]
Underfull \hbox (badness 4036) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2076] [2077]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15335--15335
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2078]
Underfull \hbox (badness 1715) in paragraph at lines 15387--15390
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15432--15434
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2079] [2080] [2081]) [2082] [2083] [2084] (./KernSmooth-pkg.tex
Chapter 15.
[2085]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2086] [2087] [2088] [2089] [2090]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2091] [2092] [2093] [2094]) (./MASS-pkg.tex
Chapter 16.
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116]
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 6559) in paragraph at lines 2694--2697
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2133] [2134] [2135]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2136] [2137]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2138] [2139] [2140]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2141]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152]
[2153]
Underfull \hbox (badness 1845) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2154] [2155] [2156] [2157] [2158] [2159] [2160]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2161] [2162] [2163]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
[2175] [2176] [2177]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2178]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2179] [2180]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2181]
Underfull \hbox (badness 1783) in paragraph at lines 6229--6233
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2182] [2183] [2184] [2185]
Underfull \vbox (badness 10000) has occurred while \output is active [2186]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2187]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2188] [2189] [2190] [2191] [2192] [2193]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2194]
Underfull \hbox (badness 10000) in paragraph at lines 7094--7096
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7149--7155
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2196] [2197]
Underfull \hbox (badness 5091) in paragraph at lines 7328--7331
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2198] [2199]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2200]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 4686) in paragraph at lines 7961--7963
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2207] [2208]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8104--8108
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219]
[2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2229]
Underfull \hbox (badness 2035) in paragraph at lines 9595--9597
[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9610--9613
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2230]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241]
[2242] [2243]) (./Matrix-pkg.tex [2244]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
Underfull \hbox (badness 10000) in paragraph at lines 41--44
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2245]
Underfull \hbox (badness 1769) in paragraph at lines 95--98
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2246]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
Underfull \hbox (badness 1147) in paragraph at lines 159--162
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2247]
Underfull \hbox (badness 10000) in paragraph at lines 257--260
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2248] [2249]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2250]
Underfull \hbox (badness 5119) in paragraph at lines 508--512
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2251] [2252]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675
 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676
 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681
 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2253]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2254] [2255] [2256]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2257] [2258]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2259pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
Underfull \hbox (badness 2285) in paragraph at lines 1220--1225
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2260]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2261]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
Underfull \hbox (badness 2277) in paragraph at lines 1388--1391
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2262]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2264]
Underfull \hbox (badness 10000) in paragraph at lines 1531--1538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1531--1538
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1582--1588
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2265]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2266]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1710--1714
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2267] [2268]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2269] [2270] [2271] [2272] [2273]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2274]
Underfull \hbox (badness 7379) in paragraph at lines 2330--2332
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2275] [2276] [2277]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2278]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2677--2682
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2279]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2280]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2281]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3012--3016
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2284]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3528--3532
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2287]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2288] [2289]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3725--3730
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3815
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2291] [2292] [2293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2294]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2295] [2296]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2297] [2298] [2299] [2300]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534
 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537
 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2301] [2302] [2303] [2304]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2305]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2306]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2307] [2308]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130
 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131
 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134
 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2309]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2310]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
Underfull \hbox (badness 10000) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5279--5282
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2311]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2312]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2313] [2314] [2315]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2317]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5757--5762
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2318]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2319]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2320]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2321]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6096--6101
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6104--6107
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2322]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6214--6224
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2323]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2326]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6524--6530
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6545--6548
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2327]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2328] [2329]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6775--6779
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2330] [2331]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 10000) in paragraph at lines 6971--6974
Underfull \hbox (badness 10000) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2332]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7152 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2333] [2334pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 7423--7426
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7426--7431
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7426--7431
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7431--7435
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7431--7435
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7441--7442
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2335] [2336]
Underfull \hbox (badness 1009) in paragraph at lines 7577--7579
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7622--7625
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2337]
Underfull \hbox (badness 6063) in paragraph at lines 7656--7659
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2339] [2340]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2341]
Underfull \hbox (badness 2635) in paragraph at lines 7912--7917
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7912--7917
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7920--7923
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2342]
Underfull \hbox (badness 3482) in paragraph at lines 7994--8000
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2343]
Underfull \hbox (badness 1867) in paragraph at lines 8114--8116
[]\T1/ptm/m/n/10 fast sim-
[2344]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2345]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241
 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Underfull \hbox (badness 2401) in paragraph at lines 8356--8366
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2346]
Underfull \hbox (badness 3179) in paragraph at lines 8427--8430
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 8517--8520
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 8593--8596
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2349]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 8719--8721
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8721--8724
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8727--8734
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2351] [2352]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820
 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823
 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829
 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Underfull \hbox (badness 3989) in paragraph at lines 8855--8865
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8855--8865
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2353] [2354]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2355]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029
 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040
 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9044--9044
 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061
 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069
 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2356]
Underfull \hbox (badness 10000) in paragraph at lines 9122--9128
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
Underfull \hbox (badness 10000) in paragraph at lines 9139--9142
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2357]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
[2358]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9233--9233
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2359] [2360]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2361] [2362]
Underfull \hbox (badness 10000) in paragraph at lines 9550--9552
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
Underfull \hbox (badness 2351) in paragraph at lines 9556--9564
[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
Underfull \hbox (badness 1325) in paragraph at lines 9556--9564
\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
[2363] [2364]
Underfull \hbox (badness 1558) in paragraph at lines 9701--9704
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2365]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2366]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                            [2367]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9931--9931
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
Underfull \hbox (badness 1616) in paragraph at lines 9966--9978
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
Underfull \hbox (badness 10000) in paragraph at lines 9983--9986
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
Underfull \hbox (badness 10000) in paragraph at lines 9992--9999
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 10000) in paragraph at lines 10005--10015
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 4660) in paragraph at lines 10005--10015
\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2368]
Underfull \hbox (badness 6032) in paragraph at lines 10032--10036
[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
Underfull \hbox (badness 10000) in paragraph at lines 10039--10041
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
Underfull \hbox (badness 10000) in paragraph at lines 10062--10063
[]\T1/ptm/m/n/10 works via
Underfull \hbox (badness 10000) in paragraph at lines 10068--10070
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
Underfull \hbox (badness 10000) in paragraph at lines 10072--10073
[]\T1/ptm/m/n/10 all work via
Underfull \hbox (badness 10000) in paragraph at lines 10080--10083
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
[2369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10098--10098
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10102--10102
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
Underfull \hbox (badness 10000) in paragraph at lines 10123--10126
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
Underfull \hbox (badness 1648) in paragraph at lines 10151--10153
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
[2370]
Underfull \hbox (badness 10000) in paragraph at lines 10159--10162
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
Underfull \hbox (badness 2591) in paragraph at lines 10159--10162
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
Underfull \hbox (badness 10000) in paragraph at lines 10170--10174
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
Underfull \hbox (badness 2828) in paragraph at lines 10170--10174
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10181--10183
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
Underfull \hbox (badness 1158) in paragraph at lines 10199--10205
[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2372] [2373]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444
 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2374]
Underfull \hbox (badness 4621) in paragraph at lines 10485--10489
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573
 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
[2376]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2377]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638
 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2378]
Underfull \hbox (badness 10000) in paragraph at lines 10784--10788
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
[2379]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2380]
Underfull \hbox (badness 10000) in paragraph at lines 10954--10956
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2381]
Underfull \hbox (badness 5036) in paragraph at lines 11010--11012
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2382]
Underfull \hbox (badness 2970) in paragraph at lines 11143--11149
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11143--11149
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2383]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
Underfull \hbox (badness 10000) in paragraph at lines 11234--11239
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11249--11251
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2384]
Underfull \vbox (badness 10000) has occurred while \output is active [2385]
Underfull \hbox (badness 2698) in paragraph at lines 11374--11380
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2386] [2387]
Underfull \hbox (badness 10000) in paragraph at lines 11467--11469
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11485--11490
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11485--11490
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11493--11498
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2388]
Underfull \hbox (badness 2057) in paragraph at lines 11565--11567
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2389]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
[2390]
Underfull \hbox (badness 5133) in paragraph at lines 11691--11695
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11691--11695
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2391]
Underfull \hbox (badness 7649) in paragraph at lines 11798--11800
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2392] [2393] [2394]
Underfull \hbox (badness 7362) in paragraph at lines 11999--12001
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2395]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2396] [2397]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2398] [2399] [2400]) (./boot-pkg.tex
Chapter 18.
[2401] [2402] [2403] [2404] [2405] [2406] [2407]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2408]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2409] [2410] [2411]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2413]
[2414]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2415]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2420] [2421] [2422] [2423] [2424]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2425] [2426] [2427]
Underfull \vbox (badness 10000) has occurred while \output is active [2428]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2429]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2430] [2431] [2432]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2433]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2434] [2435]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2436] [2437] [2438] [2439] [2440]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2441] [2442] [2443]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2444]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2445] [2446] [2447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2448] [2449] [2450] [2451] [2452] [2453] [2454]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2455] [2456]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2457] [2458] [2459]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2460]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2461] [2462]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] [2471]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2472] [2473] [2474] [2475]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2476]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2485]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2486]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2487] [2488] [2489] [2490]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2491] [2492]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2493] [2494] [2495]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2496] [2497]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2498] [2499] [2500] [2501] [2502] [2503] [2504] [2505]) (./class-pkg.tex
[2506]
Chapter 19.
[2507] [2508] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
[2518] [2519] [2520] [2521] [2522]) (./cluster-pkg.tex
Chapter 20.
[2523]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 133--142
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 133--142
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 133--142
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2524] [2525]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2526] [2527]
Underfull \vbox (badness 10000) has occurred while \output is active [2528]
[2529]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2530] [2531]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2532]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2533] [2534]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2535]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2536]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2537]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1102--1102
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2539]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1119--1119
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1157--1157
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2540]
Underfull \hbox (badness 4144) in paragraph at lines 1189--1193
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2541]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1265--1265
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1271--1271
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2542] [2543]
Underfull \hbox (badness 10000) in paragraph at lines 1410--1415
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1458--1461
[2544]
Underfull \hbox (badness 10000) in paragraph at lines 1475--1479
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1499--1499
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1509--1509
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2545]
Underfull \hbox (badness 5741) in paragraph at lines 1549--1552
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2546]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1615--1615
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2547]
Underfull \hbox (badness 1540) in paragraph at lines 1732--1740
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2548] [2549]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1823--1823
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1842--1842
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2550] [2551] [2552] [2553]
Underfull \hbox (badness 10000) in paragraph at lines 2161--2164
Underfull \hbox (badness 3179) in paragraph at lines 2175--2181
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 2333--2336
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2557]
Underfull \hbox (badness 1292) in paragraph at lines 2401--2404
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2410--2412
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2433--2436
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2558] [2559] [2560] [2561]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2649--2649
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2562] [2563] [2564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2918--2918
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2565] [2566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3021--3021
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2567] [2568] [2569]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3217--3217
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 3285--3288
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2571]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3335--3335
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572] [2573] [2574]
Underfull \hbox (badness 10000) in paragraph at lines 3521--3524
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2575]
Underfull \hbox (badness 10000) in paragraph at lines 3584--3589
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2576]
Underfull \hbox (badness 3884) in paragraph at lines 3646--3651
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3658--3661
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 3843--3846
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3874--3877
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2580]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3927--3927
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3938--3940
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2581] [2582] [2583] [2584]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4131--4131
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4133--4133
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2585] [2586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4271--4271
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4280--4280
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4282--4282
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4285--4285
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4287--4287
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4294--4294
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2587] [2588] [2589] [2590] [2591] [2592]
Underfull \hbox (badness 10000) in paragraph at lines 4652--4658
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4668--4670
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4681--4681
 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4683--4683
 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2593]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4697--4697
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2594]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2595]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2597] [2598] [2599]) (./foreign-pkg.tex [2600]
Chapter 22.
[2601]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2602] [2603]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2604]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2605] [2606] [2607]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2608]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
Underfull \hbox (badness 6001) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2609]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2610]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2611]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658
 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2612] [2613]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2614] [2615]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2616]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2621]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2622]) (./lattice-pkg.tex
Chapter 23.
[2623] [2624] [2625]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2626]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2627] [2628] [2629] [2630]
Underfull \hbox (badness 1221) in paragraph at lines 650--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2631] [2632] [2633] [2634]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2635]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2636] [2637]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2638] [2639] [2640]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2641]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2642]
Underfull \vbox (badness 10000) has occurred while \output is active [2643]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2644]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2645] [2646] [2647] [2648]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2649]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2650] [2651] [2652]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2653] [2654] [2655] [2656] [2657]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2658] [2659]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2660]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2661] [2662]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2663]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2664] [2665] [2666] [2667]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2668]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2669] [2670] [2671] [2672] [2673]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2674]
Underfull \hbox (badness 2277) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2675] [2676]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2677]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2678] [2679]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2680] [2681] [2682] [2683] [2684] [2685]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2686] [2687]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2688] [2689]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2690] [2691] [2692] [2693] [2694] [2695]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2697]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2698]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2700] [2701]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2702] [2703]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2704] [2705]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2706] [2707]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2708]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2709] [2710]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2711]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2712] [2713] [2714] [2715] [2716] [2717]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6955--6962
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2719]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
Underfull \hbox (badness 1584) in paragraph at lines 7055--7059
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2720]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2721] [2722]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2724] [2725]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
Underfull \hbox (badness 2772) in paragraph at lines 7526--7529
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2726]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2727]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2728] [2729] [2730]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2731]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2732] [2733] [2734] [2735] [2736] [2737] [2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2740] [2741]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2742]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2743]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2744]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2745] [2746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2747] [2748]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2749]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2750] [2751] [2752] [2753] [2754] [2755] [2756]
Underfull \hbox (badness 7238) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9622--9626
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2757] [2758] [2759]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2760] [2761] [2762]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088
 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2763] [2764]) (./mgcv-pkg.tex
Chapter 24.
[2765] [2766]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2767]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152
 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2768] [2769] [2770] [2771]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2772]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408
 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2773] [2774] [2775]
Underfull \hbox (badness 2922) in paragraph at lines 607--608
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2776] [2777] [2778]
Underfull \hbox (badness 1158) in paragraph at lines 753--755
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2779]
Underfull \hbox (badness 1259) in paragraph at lines 816--817
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2780]
Underfull \vbox (badness 10000) has occurred while \output is active [2781]
[2782] [2783] [2784] [2785]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2786]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171
 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178
 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1180--1180
 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1182--1182
 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2787]
[2788]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274
 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285
 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1319--1319
 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2789]
[2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2798] [2799] [2800] [2801] [2802] [2803]
Underfull \hbox (badness 1052) in paragraph at lines 2197--2205
\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2214--2214
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Underfull \hbox (badness 1728) in paragraph at lines 2226--2229
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
Underfull \hbox (badness 1142) in paragraph at lines 2239--2243
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804]
Underfull \hbox (badness 1043) in paragraph at lines 2265--2270
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2805] [2806]
Underfull \hbox (badness 1043) in paragraph at lines 2428--2434
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2807] [2808]
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2809]
Underfull \vbox (badness 10000) has occurred while \output is active [2810]
Underfull \vbox (badness 10000) has occurred while \output is active [2811]
Underfull \vbox (badness 10000) has occurred while \output is active [2812]
[2813] [2814] [2815] [2816] [2817] [2818] [2819]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3223--3223
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2820] [2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 5189) in paragraph at lines 3584--3588
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2826] [2827]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2828]
[2829] [2830]
Underfull \hbox (badness 1184) in paragraph at lines 3870--3874
[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2831] [2832] [2833] [2834] [2835] [2836] [2837]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2838] [2839] [2840]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466
 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2841]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
[2842]
Underfull \hbox (badness 1142) in paragraph at lines 4591--4595
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2843]
Underfull \hbox (badness 10000) in paragraph at lines 4660--4669
[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2844] [2845]
Underfull \hbox (badness 5970) in paragraph at lines 4777--4783
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1418) in paragraph at lines 4777--4783
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2846]
Underfull \vbox (badness 10000) has occurred while \output is active [2847]
[2848] [2849]
Underfull \hbox (badness 1577) in paragraph at lines 5057--5060
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2850] [2851] [2852] [2853] [2854] [2855] [2856]
Underfull \hbox (badness 6708) in paragraph at lines 5453--5454
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2857]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502
 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527
 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5556--5556
 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2859]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2860] [2861] [2862] [2863] [2864] [2865]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933
 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5935--5935
 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
Underfull \hbox (badness 1142) in paragraph at lines 5956--5960
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2866] [2867] [2868] [2869] [2870] [2871]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219
 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273
 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2872] [2873] [2874] [2875]
Underfull \vbox (badness 10000) has occurred while \output is active [2876]
Underfull \vbox (badness 10000) has occurred while \output is active [2877]
[2878] [2879]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6729--6729
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888]
Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2889] [2890]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359
 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2891] [2892]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422
 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7441--7441
 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2893]
[2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904]
[2905] [2906] [2907] [2908] [2909] [2910]
Underfull \vbox (badness 10000) has occurred while \output is active [2911]
[2912]
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2913]
Underfull \hbox (badness 10000) in paragraph at lines 8717--8720
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 8717--8720
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2914] [2915] [2916]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8938--8938
 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8941--8941
 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2917] [2918] [2919]
Underfull \hbox (badness 1629) in paragraph at lines 9099--9104
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2920] [2921] [2922] [2923]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310
 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2924] [2925]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474
 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2926] [2927] [2928] [2929]
Underfull \vbox (badness 10000) has occurred while \output is active [2930]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2931]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9780--9782
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
Underfull \hbox (badness 1975) in paragraph at lines 9786--9791
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2932]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2933]
Underfull \hbox (badness 10000) in paragraph at lines 9939--9942
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
Underfull \hbox (badness 2057) in paragraph at lines 9939--9942
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2934] [2935]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2936] [2937] [2938] [2939]
Underfull \hbox (badness 1946) in paragraph at lines 10247--10254
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
Underfull \hbox (badness 2846) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2940]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2941] [2942] [2943] [2944] [2945]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637
 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[2946] [2947] [2948] [2949] [2950] [2951]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985
 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 
Underfull \hbox (badness 10000) in paragraph at lines 10998--11002
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2952]
Underfull \hbox (badness 10000) in paragraph at lines 11038--11042
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2953] [2954] [2955]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2956]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2957] [2958] [2959]
Underfull \vbox (badness 10000) has occurred while \output is active [2960]
Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2961] [2962]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703
 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727
 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732
 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2965]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738
 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739
 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2966]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[2967] [2968]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2969]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[2970] [2971] [2972]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2973] [2974] [2975] [2976]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 12468--12470
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2978] [2979]
Underfull \vbox (badness 10000) has occurred while \output is active [2980]
Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12627--12630
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 12627--12630
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2981]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 12754--12760
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2983] [2984] [2985]
Underfull \vbox (badness 10000) has occurred while \output is active [2986]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2987]
Underfull \hbox (badness 10000) in paragraph at lines 13071--13079
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2988]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2989] [2990] [2991] [2992]
Underfull \hbox (badness 3396) in paragraph at lines 13358--13361
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2993]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2994] [2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13627--13630
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
[2998]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3004]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3005] [3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3007] [3008]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019]
[3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3029] [3030] [3031] [3032] [3033]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3034] [3035] [3036]) (./nlme-pkg.tex
Chapter 25.
[3037]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3039] [3040] [3041] [3042] [3043]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3044] [3045]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3054]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3055] [3056] [3057] [3058] [3059] [3060] [3061]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3062]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3063] [3064] [3065] [3066] [3067]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3069]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3070] [3071]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091]
[3092]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3093] [3094] [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103]
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114]
[3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3117] [3118] [3119] [3120] [3121] [3122] [3123]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3133]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3134]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3136] [3137] [3138] [3139]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3140]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3141]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3142]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3143] [3144] [3145]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3146]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3147] [3148] [3149]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3150] [3151] [3152]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3153] [3154] [3155]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3164] [3165] [3166] [3167] [3168]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3169]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3170] [3171] [3172] [3173] [3174]
[3175] [3176] [3177] [3178] [3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3182]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3183] [3184] [3185] [3186]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3187]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9750--9753
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3196] [3197] [3198]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3199]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3200] [3201] [3202]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3203] [3204]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3205]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3206] [3207] [3208] [3209]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3210] [3211] [3212] [3213] [3214] [3215]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3216] [3217] [3218] [3219] [3220] [3221]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3222] [3223] [3224] [3225]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3226] [3227] [3228] [3229] [3230]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3231] [3232]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3233]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3243] [3244] [3245] [3246] [3247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3248]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3249]
Underfull \hbox (badness 1838) in paragraph at lines 13734--13741
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13734--13741
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13798--13801
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13798--13801
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13826--13829
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13826--13829
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3252]
Underfull \hbox (badness 1472) in paragraph at lines 13931--13938
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3258] [3259] [3260] [3261]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3271] [3272] [3273]
[3274] [3275] [3276] [3277] [3278] [3279] [3280]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3281] [3282] [3283]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3284] [3285] [3286] [3287] [3288]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3289]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3290] [3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3297] [3298] [3299] [3300] [3301]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3302]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
Underfull \hbox (badness 10000) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3303] [3304] [3305] [3306]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3314]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3315]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3317]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18245--18250
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 3579) in paragraph at lines 18380--18385
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3320] [3321]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18658--18667
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3333]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3334] [3335] [3336]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3338] [3339]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3340]) (./rpart-pkg.tex
Chapter 27.
[3341] [3342] [3343] [3344]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3345] [3346] [3347] [3348]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3349] [3350]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3351] [3352]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3353]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3354] [3355] [3356]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3357]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3358]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3359] [3360] [3361] [3362] [3363] [3364]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3365] [3366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3367] [3368] [3369]) (./spatial-pkg.tex [3370]
Chapter 28.
[3371] [3372] [3373] [3374] [3375] [3376]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387]
[3388] [3389]) (./survival-pkg.tex [3390]
Chapter 29.
[3391] [3392]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3393] [3394]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3395] [3396]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3397]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3398] [3399]
Underfull \vbox (badness 10000) has occurred while \output is active [3400]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3401] [3402]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3403] [3404] [3405]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3406] [3407]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3408]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                  
Underfull \vbox (badness 2698) has occurred while \output is active [3409]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271
 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3410] [3411]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3412] [3413] [3414] [3415] [3416]
Underfull \hbox (badness 1337) in paragraph at lines 1799--1803
[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854
 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3418] [3419] [3420] [3421] [3422] [3423] [3424]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351
 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3425] [3426] [3427]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3428] [3429] [3430] [3431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3432]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894
 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
Underfull \hbox (badness 1389) in paragraph at lines 2908--2910
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3433]
Underfull \hbox (badness 1048) in paragraph at lines 2963--2965
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3434]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037
 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3435] [3436]
Underfull \vbox (badness 10000) has occurred while \output is active [3437]
Underfull \vbox (badness 10000) has occurred while \output is active [3438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3439] [3440] [3441] [3442] [3443]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560
 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3444]
Underfull \vbox (badness 10000) has occurred while \output is active [3445]
[3446] [3447] [3448] [3449] [3450]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977
 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3451] [3452]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3453]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3454]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299
 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3455]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3456] [3457]
Underfull \hbox (badness 1852) in paragraph at lines 4533--4535
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3458] [3459]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669
 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3460] [3461] [3462]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3464] [3465] [3466] [3467] [3468]
Underfull \vbox (badness 2126) has occurred while \output is active [3469]
[3470] [3471]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 1043) in paragraph at lines 5560--5563
\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3472] [3473] [3474] [3475] [3476]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3477] [3478]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3479] [3480] [3481] [3482] [3483]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3484] [3485] [3486] [3487]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3488] [3489] [3490]
Underfull \hbox (badness 1253) in paragraph at lines 6915--6918
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3491] [3492]
Underfull \hbox (badness 10000) in paragraph at lines 7041--7050
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
Underfull \hbox (badness 3758) in paragraph at lines 7041--7050
\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3493]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137
 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3494]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
Underfull \hbox (badness 1038) in paragraph at lines 7197--7203
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3495]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3496]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3497] [3498] [3499]
Underfull \hbox (badness 10000) in paragraph at lines 7560--7565
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
[3500]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3501] [3502]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3503] [3504] [3505]
Underfull \hbox (badness 3058) in paragraph at lines 7969--7974
[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
Underfull \hbox (badness 7759) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
Underfull \hbox (badness 2913) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
Underfull \hbox (badness 4353) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
[3506]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3507] [3508] [3509] [3510]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3511]
Underfull \hbox (badness 1354) in paragraph at lines 8422--8426
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3512] [3513]
Underfull \hbox (badness 2035) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 8597--8604
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3514]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3515] [3516] [3517]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3518] [3519]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8965--8965
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3520] [3521] [3522] [3523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267
 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9268--9268
 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3524]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274
 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9276--9276
 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3525] [3526] [3527] [3528] [3529] [3530] [3531]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727
 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3532] [3533] [3534])
No file fullrefman.ind.
(./fullrefman.aux)
Package rerunfilecheck Warning: File `fullrefman.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.
 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts
/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/c
ourier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmri8a.pfb>
Output written on fullrefman.pdf (3537 pages, 9029797 bytes).
Transcript written on fullrefman.log.
This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
Scanning input file fullrefman.idx............................done (24183 entries accepted, 76 rejected).
Sorting entries................................................................................................................................................................................................................................................................................done (402138 comparisons).
Generating output file fullrefman.ind..........................done (25141 lines written, 118 warnings).
Output written in fullrefman.ind.
Transcript written in fullrefman.ilg.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo
aded.
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.
) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./fullrefman.out) (./fullrefman.out)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texliv
e/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4]
[5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20]
[21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49]) [50]
[1] [2] (./base-pkg.tex
Chapter 1.
[3] [4]
Underfull \hbox (badness 6741) in paragraph at lines 135--141
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 .
Underfull \hbox (badness 4805) in paragraph at lines 135--141
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10
 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is
Underfull \hbox (badness 4316) in paragraph at lines 135--141
\T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-
wise, it is \T1/pcr/m/n/10 (double.base ^
Underfull \hbox (badness 5050) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It
Underfull \hbox (badness 1028) in paragraph at lines 141--149
\T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/pcr/m/n/10 double.base
Underfull \hbox (badness 2980) in paragraph at lines 141--149
\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 141--149
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As
Underfull \hbox (badness 1668) in paragraph at lines 152--159
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5] [6] [7]
Underfull \hbox (badness 10000) in paragraph at lines 339--342
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8] [9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 534--540
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13]
[14] [15]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
Underfull \hbox (badness 1838) in paragraph at lines 1178--1181
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[21] [22] [23] [24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670
 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
Underfull \hbox (badness 1303) in paragraph at lines 1698--1701
[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[28] [29]
Underfull \hbox (badness 10000) in paragraph at lines 1816--1818
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[30] [31]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
Underfull \hbox (badness 10000) in paragraph at lines 1991--1993
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[32] [33] [34] [35]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[38]
Underfull \hbox (badness 1107) in paragraph at lines 2460--2462
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326
 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327
 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334
 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335
 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012
 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
Underfull \hbox (badness 4927) in paragraph at lines 4267--4271
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 4267--4271
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
Underfull \hbox (badness 1199) in paragraph at lines 4596--4602
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
Underfull \hbox (badness 2573) in paragraph at lines 4607--4610
[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[70] [71]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4766--4766
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[72] [73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5019--5021
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5416--5424
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[82] [83] [84] [85] [86] [87] [88] [89]
Underfull \hbox (badness 1796) in paragraph at lines 5979--5987
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[90] [91] [92]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6175--6175
 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6176--6176
 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6311--6315
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
Underfull \hbox (badness 1635) in paragraph at lines 6353--6356
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6357--6360
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[95]
Underfull \hbox (badness 1308) in paragraph at lines 6388--6396
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[96] [97]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6542--6542
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6584--6586
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6732--6735
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6732--6735
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[101] [102]
Underfull \hbox (badness 1406) in paragraph at lines 6914--6920
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 6934--6936
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
Underfull \hbox (badness 1067) in paragraph at lines 6976--6983
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7168--7168
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
Underfull \hbox (badness 1231) in paragraph at lines 7293--7299
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7506
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7649--7649
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7887--7887
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
Underfull \hbox (badness 8132) in paragraph at lines 7988--7992
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7988--7992
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 8007--8017
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8007--8017
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[119]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8039--8043
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[120] [121] [122] [123] [124] [125]
Underfull \hbox (badness 1629) in paragraph at lines 8525--8537
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8525--8537
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8788
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
Underfull \hbox (badness 10000) in paragraph at lines 8972--8976
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[132] [133]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9063--9063
 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9065--9065
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9090--9090
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9091--9091
 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
Underfull \hbox (badness 5403) in paragraph at lines 9209--9211
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[136] [137] [138]
Underfull \hbox (badness 1603) in paragraph at lines 9439--9442
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10045--10050
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10100--10100
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10101--10101
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
Underfull \hbox (badness 1168) in paragraph at lines 10203--10208
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[150]
Underfull \hbox (badness 10000) in paragraph at lines 10242--10248
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10249--10252
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[151] [152]
Underfull \hbox (badness 2828) in paragraph at lines 10408--10412
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10408--10412
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10441--10441
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10514--10514
 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[155] [156]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10658--10658
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
Underfull \hbox (badness 6396) in paragraph at lines 10847--10855
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
Underfull \hbox (badness 10000) in paragraph at lines 10856--10858
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11073--11076
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[163] [164] [165] [166] [167] [168] [169] [170] [171]
Underfull \hbox (badness 5288) in paragraph at lines 11771--11773
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
Underfull \hbox (badness 3039) in paragraph at lines 11781--11786
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 10000) in paragraph at lines 11841--11843
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
Underfull \hbox (badness 4569) in paragraph at lines 11963--11967
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 11963--11967
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12078--12080
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12919--12919
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 2221) in paragraph at lines 13365--13374
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13365--13374
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13626--13628
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
Underfull \hbox (badness 2573) in paragraph at lines 13741--13743
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13891--13893
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14004
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14011--14014
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 14032--14032
 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 14055--14055
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
Underfull \hbox (badness 10000) in paragraph at lines 14147--14150
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14157--14157
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
Underfull \hbox (badness 10000) in paragraph at lines 14223--14226
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14240--14240
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 1472) in paragraph at lines 14293--14300
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14293--14300
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14301--14305
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[208] [209] [210]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14464--14464
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14465--14465
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14695--14695
 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 14698--14698
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
Underfull \hbox (badness 1168) in paragraph at lines 14782--14786
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14782--14786
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
Underfull \hbox (badness 6944) in paragraph at lines 14880--14883
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[216]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14905--14905
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
Underfull \hbox (badness 10000) in paragraph at lines 15043--15045
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15063--15063
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15069--15069
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
Underfull \hbox (badness 2790) in paragraph at lines 15076--15079
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 1024) in paragraph at lines 15107--15111
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[220]
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
[]\T1/ptm/m/n/10 The im-ple-men-ta-tion has \T1/pcr/m/n/10 formatC() \T1/ptm/m/
n/10 call-ing \T1/pcr/m/n/10 prettyNum()
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
\T1/ptm/m/n/10 (only if \T1/pcr/m/n/10 zero.print \T1/ptm/m/n/10 is not \T1/pcr
/m/n/10 NULL\T1/ptm/m/n/10 ) which it-self calls
Underfull \hbox (badness 2818) in paragraph at lines 15192--15194
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15203--15211
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[221] [222]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15304--15304
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15326--15326
 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16143--16143
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[235] [236]
Underfull \hbox (badness 2418) in paragraph at lines 16252--16256
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16259--16262
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16294--16301
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[237] [238] [239] [240]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16540--16540
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16565--16572
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[241] [242] [243] [244]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16834--16834
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16863--16863
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [245]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16914--16914
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[246] [247] [248] [249] [250]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17279--17279
 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[251] [252] [253] [254]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17533--17533
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257]
Underfull \hbox (badness 2435) in paragraph at lines 17796--17798
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[258]
Underfull \hbox (badness 2285) in paragraph at lines 17862--17864
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17870--17870
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[259]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17880--17880
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 17900--17900
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 18040--18040
 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18043--18043
 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18049--18049
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[262] [263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 18176--18176
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18184--18184
 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[264] [265] [266]
Underfull \hbox (badness 10000) in paragraph at lines 18389--18391
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[267]
Underfull \hbox (badness 4217) in paragraph at lines 18473--18482
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18488--18504
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[268] [269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18907--18910
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[275] [276]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19030--19030
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19165--19167
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 19214--19214
 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19215--19215
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1975) in paragraph at lines 19793--19796
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[288] [289] [290] [291] [292] [293]
Underfull \hbox (badness 1077) in paragraph at lines 20188--20193
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[294]
Underfull \hbox (badness 10000) in paragraph at lines 20202--20209
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20276--20280
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20425--20429
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 20425--20429
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20430--20437
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
[298] [299]
Underfull \hbox (badness 10000) in paragraph at lines 20561--20568
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[300]
Underfull \hbox (badness 10000) in paragraph at lines 20682--20686
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[301]
Underfull \hbox (badness 5161) in paragraph at lines 20752--20757
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[302] [303] [304]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20919--20919
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20923--20923
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[305]
Underfull \hbox (badness 3343) in paragraph at lines 20979--20983
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[306]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21065--21065
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21076--21076
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[307] [308]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21187--21187
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21190--21190
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
Underfull \hbox (badness 6380) in paragraph at lines 21235--21240
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[309] [310]
Underfull \hbox (badness 2564) in paragraph at lines 21326--21329
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21356--21356
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[311] [312]
Underfull \hbox (badness 1400) in paragraph at lines 21524--21528
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[313] [314] [315]
Underfull \hbox (badness 2469) in paragraph at lines 21694--21700
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
Underfull \hbox (badness 4531) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[316] [317] [318] [319] [320] [321] [322] [323] [324]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22321--22321
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22322--22322
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 22325--22325
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[325] [326]
Underfull \hbox (badness 1655) in paragraph at lines 22449--22453
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[327] [328] [329] [330]
Underfull \hbox (badness 2277) in paragraph at lines 22698--22701
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[331] [332] [333] [334] [335] [336] [337] [338]
Underfull \hbox (badness 1484) in paragraph at lines 23263--23271
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 23263--23271
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[339] [340]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23340--23340
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[341] [342] [343] [344] [345] [346] [347]
Underfull \hbox (badness 1448) in paragraph at lines 23845--23853
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[348] [349]
Underfull \hbox (badness 3849) in paragraph at lines 23959--23964
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[350]
Underfull \hbox (badness 7308) in paragraph at lines 24036--24042
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 10000) in paragraph at lines 24036--24042
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 1210) in paragraph at lines 24036--24042
[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[351] [352]
Underfull \hbox (badness 10000) in paragraph at lines 24199--24201
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[353] [354] [355]
Underfull \hbox (badness 6188) in paragraph at lines 24418--24421
[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 2197) in paragraph at lines 24902--24906
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24902--24906
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[363]
Underfull \hbox (badness 2846) in paragraph at lines 24916--24920
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
Underfull \hbox (badness 1990) in paragraph at lines 24916--24920
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24958--24958
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24962--24962
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[364]
Underfull \hbox (badness 10000) in paragraph at lines 25010--25016
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25010--25016
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 25023--25025
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25074--25074
 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[366] [367] [368]
Underfull \hbox (badness 8189) in paragraph at lines 25267--25273
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[369] [370] [371]
Underfull \hbox (badness 1694) in paragraph at lines 25489--25492
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[372] [373] [374]
Underfull \hbox (badness 1603) in paragraph at lines 25736--25738
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[375] [376]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25863--25871
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[377] [378]
Underfull \hbox (badness 3271) in paragraph at lines 26070--26073
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[379] [380] [381]
Underfull \hbox (badness 3138) in paragraph at lines 26370--26376
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[382]
Underfull \hbox (badness 1194) in paragraph at lines 26383--26386
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 1389) in paragraph at lines 26409--26411
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 26429--26435
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26444--26449
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Underfull \hbox (badness 1009) in paragraph at lines 26462--26465
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[383]
Underfull \hbox (badness 10000) in paragraph at lines 26478--26481
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 26500--26507
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[384] [385] [386] [387]
Underfull \vbox (badness 10000) has occurred while \output is active [388]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26844--26844
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[389] [390]
Underfull \hbox (badness 10000) in paragraph at lines 27004--27007
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
Underfull \hbox (badness 1062) in paragraph at lines 27004--27007
\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[391] [392] [393]
Underfull \hbox (badness 10000) in paragraph at lines 27273--27279
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 27273--27279
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
[394]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27295--27295
 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27307--27307
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[395] [396] [397] [398] [399] [400] [401]
Underfull \hbox (badness 1817) in paragraph at lines 27741--27745
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[402]
Underfull \hbox (badness 1796) in paragraph at lines 27809--27812
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[403] [404] [405]
Underfull \hbox (badness 10000) in paragraph at lines 28009--28012
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[406] [407] [408] [409] [410] [411] [412] [413] [414] [415]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28686--28686
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[416] [417] [418] [419]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28952--28952
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28963--28963
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28969--28969
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28970--28970
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28973--28973
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[420]
Underfull \hbox (badness 7415) in paragraph at lines 29048--29052
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[421]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29069--29069
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 29115--29115
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[422] [423]
Underfull \hbox (badness 3713) in paragraph at lines 29238--29249
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[424]
Underfull \hbox (badness 1248) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
Underfull \hbox (badness 10000) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[425] [426]
Underfull \hbox (badness 1533) in paragraph at lines 29500--29503
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[427] [428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29645--29645
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29663--29674
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[430] [431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29807--29807
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29809--29809
 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29810--29810
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29811--29811
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29812--29812
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29819--29819
 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[432] [433] [434] [435] [436] [437]
Underfull \hbox (badness 4048) in paragraph at lines 30166--30171
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
Underfull \hbox (badness 1824) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[438] [439] [440] [441] [442] [443] [444] [445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30707--30707
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 7558) in paragraph at lines 31209--31213
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31219--31221
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
[452]
Underfull \hbox (badness 5417) in paragraph at lines 31224--31227
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31228--31230
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31231--31233
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31636--31640
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31980--31980
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31983--31983
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32367--32367
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[470] [471] [472] [473] [474] [475]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32802--32802
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[476]
Underfull \hbox (badness 1158) in paragraph at lines 32906--32911
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[477]
Underfull \hbox (badness 10000) in paragraph at lines 32933--32939
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1762) in paragraph at lines 32933--32939
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[478] [479]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33091--33091
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[480] [481] [482]
Underfull \hbox (badness 8151) in paragraph at lines 33351--33354
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[483] [484] [485] [486]
Underfull \hbox (badness 1210) in paragraph at lines 33586--33588
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498]
[499] [500]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34523--34523
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[501] [502] [503]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34775--34775
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34777--34777
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[504]
Underfull \hbox (badness 4954) in paragraph at lines 34820--34826
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 34820--34826
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[505] [506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34931--34931
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35259--35259
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
[511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35274--35274
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[512] [513] [514] [515] [516] [517]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35715--35715
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35716--35716
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[518] [519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35980--35980
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
Underfull \hbox (badness 6110) in paragraph at lines 36064--36074
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 36064--36074
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1460) in paragraph at lines 36120--36127
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[523] [524] [525] [526]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 36397--36397
 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[527] [528] [529] [530] [531] [532] [533] [534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36959--36959
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[535] [536] [537] [538]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 37207--37207
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[539]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37251--37251
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[540] [541] [542] [543] [544] [545]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37685--37685
 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37688--37688
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[546]
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[547]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37792--37792
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[548] [549] [550] [551]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38093--38093
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[552]
Underfull \vbox (badness 7777) has occurred while \output is active [553]
[554]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38258--38258
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38296--38296
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
Underfull \hbox (badness 4792) in paragraph at lines 38345--38350
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 38345--38350
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[556]
Underfull \hbox (badness 2452) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[557] [558] [559]
Underfull \hbox (badness 10000) in paragraph at lines 38623--38627
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 38638--38641
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[560] [561]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38770--38770
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[562]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38840--38840
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[563] [564] [565]
Underfull \hbox (badness 1082) in paragraph at lines 38984--38987
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[566] [567]
Underfull \hbox (badness 1038) in paragraph at lines 39175--39178
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[568] [569] [570] [571] [572] [573]
Underfull \hbox (badness 1442) in paragraph at lines 39538--39542
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[574] [575] [576]
Underfull \hbox (badness 4096) in paragraph at lines 39784--39787
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[577] [578]
Underfull \hbox (badness 7888) in paragraph at lines 39898--39902
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[579] [580]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40052--40052
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40054--40054
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
[581]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40056--40056
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 40069--40071
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[582]
Underfull \hbox (badness 10000) in paragraph at lines 40149--40152
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[583] [584]
Underfull \hbox (badness 3872) in paragraph at lines 40267--40270
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[585]
Underfull \hbox (badness 5475) in paragraph at lines 40333--40337
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 10000) in paragraph at lines 40751--40758
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40807--40816
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40807--40816
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 2503) in paragraph at lines 40817--40825
\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[592]
Underfull \hbox (badness 1337) in paragraph at lines 40883--40891
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40892--40895
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[593]
Underfull \hbox (badness 3460) in paragraph at lines 40946--40949
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 40950--40952
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40959--40959
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[594] [595] [596]
Underfull \hbox (badness 10000) in paragraph at lines 41176--41178
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[597] [598]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41298--41298
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41300--41300
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [599]
[600] [601] [602] [603]
Underfull \hbox (badness 6542) in paragraph at lines 41662--41664
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[604] [605]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41781--41781
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[606]
Underfull \hbox (badness 1708) in paragraph at lines 41849--41857
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 41849--41857
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 4859) in paragraph at lines 41879--41884
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[607]
Underfull \hbox (badness 3895) in paragraph at lines 41941--41953
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 41941--41953
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[608] [609] [610] [611] [612]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 42264--42264
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[613] [614] [615] [616] [617] [618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42731--42731
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[619]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42740--42740
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[620]
Underfull \hbox (badness 1803) in paragraph at lines 42865--42868
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
[621]
Underfull \hbox (badness 3471) in paragraph at lines 42869--42876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[622] [623] [624]
Underfull \hbox (badness 3668) in paragraph at lines 43084--43086
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[625]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 43188--43188
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[626]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43263--43263
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 43271--43271
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[627] [628]
Underfull \hbox (badness 6220) in paragraph at lines 43401--43406
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 43401--43406
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
[629]
Underfull \hbox (badness 10000) in paragraph at lines 43422--43427
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
Underfull \hbox (badness 4229) in paragraph at lines 43422--43427
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[630]
Underfull \hbox (badness 2818) in paragraph at lines 43512--43518
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[631]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 43547--43547
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[632]
Underfull \hbox (badness 1622) in paragraph at lines 43641--43643
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[633] [634] [635] [636] [637]
Underfull \hbox (badness 2846) in paragraph at lines 44004--44008
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44044--44044
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
Underfull \hbox (badness 3209) in paragraph at lines 44065--44069
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[639]) (./compiler-pkg.tex [640]
Chapter 2.
[641]
Underfull \hbox (badness 2884) in paragraph at lines 105--119
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 105--119
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
Underfull \vbox (badness 1033) has occurred while \output is active [651]
[652] [653] [654] [655]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 702--705
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[660] [661]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1146--1149
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1544
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1541--1544
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[669] [670] [671]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1730--1733
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681] [682] [683] [684] [685] [686]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[688]
Underfull \vbox (badness 1789) has occurred while \output is active [689]
[690]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[691] [692]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[704]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
Underfull \hbox (badness 10000) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[725] [726]
Underfull \hbox (badness 10000) in paragraph at lines 379--387
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
Underfull \hbox (badness 1748) in paragraph at lines 379--387
\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[727] [728]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[738] [739]
Underfull \hbox (badness 10000) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
Underfull \hbox (badness 1173) in paragraph at lines 1322--1325
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[741] [742] [743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1565) in paragraph at lines 1810--1815
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1810--1815
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[749]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
Underfull \hbox (badness 1184) in paragraph at lines 1934--1944
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 1934--1944
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[750] [751]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[752] [753]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
Underfull \hbox (badness 2326) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
Underfull \hbox (badness 2318) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
Underfull \hbox (badness 2460) in paragraph at lines 2341--2351
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
Underfull \hbox (badness 1221) in paragraph at lines 2341--2351
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[756] [757]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
Underfull \vbox (badness 10000) has occurred while \output is active [758]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560
 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561
 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829
Underfull \vbox (badness 10000) has occurred while \output is active [764]
[765] [766] [767] [768]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161
 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3246--3246
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
Underfull \hbox (badness 1264) in paragraph at lines 3384--3389
\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[772] [773] [774]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545
 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
Underfull \hbox (badness 8170) in paragraph at lines 3571--3574
[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[775]
Underfull \hbox (badness 10000) in paragraph at lines 3655--3659
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space&
oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
Underfull \hbox (badness 5260) in paragraph at lines 3785--3788
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
Underfull \hbox (badness 5939) in paragraph at lines 4113--4118
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
Underfull \hbox (badness 3612) in paragraph at lines 4514--4519
\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
Underfull \hbox (badness 1348) in paragraph at lines 4828--4831
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[793]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
Underfull \hbox (badness 7522) in paragraph at lines 4892--4898
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[794]
Underfull \hbox (badness 1112) in paragraph at lines 4923--4927
[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[795]
Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[796] [797] [798]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
Underfull \hbox (badness 7397) in paragraph at lines 5256--5260
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[799] [800]
Underfull \hbox (badness 1552) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5390--5392
[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5422--5428
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[801]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[802] [803]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
Underfull \hbox (badness 10000) in paragraph at lines 5747--5749
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[807] [808] [809] [810] [811]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458
 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465
 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 6728--6733
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1803) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[822]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833
 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
Underfull \hbox (badness 5954) in paragraph at lines 6872--6875
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https :
[824]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
Underfull \hbox (badness 10000) in paragraph at lines 7084--7091
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7084--7091
\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[827]
Underfull \hbox (badness 5607) in paragraph at lines 7168--7172
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
Underfull \hbox (badness 5637) in paragraph at lines 7345--7351
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
[830]
Underfull \hbox (badness 1721) in paragraph at lines 7378--7381
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[831] [832]
Underfull \hbox (badness 1231) in paragraph at lines 7546--7548
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.
Underfull \hbox (badness 4647) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[837] [838] [839]
Underfull \hbox (badness 3792) in paragraph at lines 177--180
[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[840]
Underfull \hbox (badness 1412) in paragraph at lines 287--292
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[844] [845]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846] [847]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 694--698
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[848]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[849]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818
 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[850] [851]
Underfull \hbox (badness 10000) in paragraph at lines 960--964
[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977
 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979
 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855] [856] [857] [858]
Underfull \hbox (badness 1024) in paragraph at lines 1425--1433
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1459--1461
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1530--1530
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1536--1536
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1537--1537
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
Underfull \hbox (badness 10000) in paragraph at lines 1837--1843
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[865]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1874--1874
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1883--1883
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1968--1968
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2097--2097
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2102--2102
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2376--2376
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
Underfull \hbox (badness 1009) in paragraph at lines 2388--2395
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[874]
Underfull \hbox (badness 7273) in paragraph at lines 2470--2474
[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2483--2483
 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
Underfull \hbox (badness 1226) in paragraph at lines 2878--2882
\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2931--2931
 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[882]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2935--2935
 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
Underfull \hbox (badness 10000) in paragraph at lines 2987--2990
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[883] [884] [885]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3192--3192
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3197--3197
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3522--3522
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3541--3541
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[891]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3545--3545
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[892] [893]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3722--3722
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3723--3723
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3762--3762
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [895]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3814--3814
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3822--3822
 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3832--3832
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
Underfull \hbox (badness 10000) in paragraph at lines 3895--3899
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[897] [898]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4006--4006
 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[899] [900] [901]
Underfull \hbox (badness 3930) in paragraph at lines 4213--4215
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[902] [903] [904] [905] [906]
Underfull \hbox (badness 1286) in paragraph at lines 4524--4527
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[907]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4629--4629
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4634--4634
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[908]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4678--4678
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
Underfull \hbox (badness 1264) in paragraph at lines 4752--4765
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[910] [911]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4895
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[912]
Underfull \hbox (badness 10000) in paragraph at lines 5020--5023
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf, id=2987
6, 289.08pt x 289.08pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf>
[913 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 5081--5083
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf, id=2988
9, 259.97125pt x 332.24126pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [914]
[915 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/oma.pdf>]
[916]
Underfull \hbox (badness 10000) in paragraph at lines 5271--5273
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[917]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5327--5327
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5328--5328
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5693--5693
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5694--5694
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
Underfull \hbox (badness 1360) in paragraph at lines 5745--5749
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[924] [925] [926] [927] [928] [929] [930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6179--6179
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6185--6185
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
Underfull \hbox (badness 10000) in paragraph at lines 6612--6614
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
Underfull \hbox (badness 1028) in paragraph at lines 6706--6708
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf, id=3030
4, 361.35pt x 50.1875pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750
[][] 
[939 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6843--6843
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6874--6874
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [941]
[942]
Underfull \hbox (badness 10000) in paragraph at lines 6996--6998
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7023--7023
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7029--7029
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
Underfull \hbox (badness 2600) in paragraph at lines 7089--7091
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[944] [945] [946] [947]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7321--7321
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7708--7708
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7712--7712
 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7724--7724
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[955] [956] [957] [958] [959]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8073--8073
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8076--8076
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8080--8080
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8251--8251
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8252--8252
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[963] [964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8356--8356
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
Underfull \hbox (badness 2080) in paragraph at lines 8367--8372
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[965]
Underfull \hbox (badness 1112) in paragraph at lines 8415--8419
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[966]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8475--8475
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8490--8490
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8621--8621
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8806--8806
 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[971]
Underfull \hbox (badness 10000) in paragraph at lines 8834--8836
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
Underfull \hbox (badness 1584) in paragraph at lines 8868--8874
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8916 \HeaderA{units}{Graphical Units}{units}
                                               [973]
Underfull \hbox (badness 1205) in paragraph at lines 8981--8983
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 9100--9100
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
Underfull \hbox (badness 10000) in paragraph at lines 476--482
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
Underfull \hbox (badness 1024) in paragraph at lines 476--482
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[985] [986] [987] [988] [989] [990] [991] [992] [993] [994]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
Underfull \hbox (badness 1430) in paragraph at lines 1166--1171
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[995] [996] [997] [998]
Underfull \hbox (badness 3219) in paragraph at lines 1380--1383
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[999] [1000] [1001] [1002] [1003] [1004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1982--1982
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1983--1983
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
Underfull \hbox (badness 2961) in paragraph at lines 2018--2023
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1009]
Underfull \hbox (badness 1430) in paragraph at lines 2077--2082
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
Underfull \hbox (badness 4479) in paragraph at lines 2106--2109
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[1010] [1011] [1012]
Underfull \hbox (badness 2894) in paragraph at lines 2313--2320
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[1013] [1014] [1015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
Underfull \hbox (badness 1430) in paragraph at lines 2481--2486
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1016]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540
 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
[1019]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1020] [1021] [1022]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1023] [1024] [1025] [1026] [1027]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028] [1029]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
Underfull \hbox (badness 2799) in paragraph at lines 3411--3417
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1030] [1031]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1035]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747
 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046]
[1047]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1048]
Underfull \hbox (badness 1430) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1049] [1050] [1051]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061]
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
Underfull \hbox (badness 6859) in paragraph at lines 6056--6062
[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
Underfull \hbox (badness 10000) in paragraph at lines 6056--6062
\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1072] [1073] [1074] [1075] [1076]
Underfull \hbox (badness 1867) in paragraph at lines 6366--6368
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1077]
Underfull \hbox (badness 10000) in paragraph at lines 6403--6409
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1078] [1079]
Underfull \hbox (badness 1371) in paragraph at lines 6535--6538
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
[1080] [1081] [1082]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1087] [1088] [1089]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1090] [1091]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558
 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568
 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619
 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1093]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637
 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640
 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657
 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672
 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
Underfull \vbox (badness 10000) has occurred while \output is active [1094]
[1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105]
[1106] [1107] [1108]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1111] [1112] [1113]
Underfull \hbox (badness 1478) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
[1114] [1115]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360
 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
Underfull \hbox (badness 1194) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1119]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
Underfull \hbox (badness 10000) in paragraph at lines 3403--3408
[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
Underfull \hbox (badness 6268) in paragraph at lines 3403--3408
\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1130] [1131]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1132]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651
[]
[1133] [1134]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
Underfull \hbox (badness 10000) in paragraph at lines 3809--3810
[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
Underfull \hbox (badness 10000) in paragraph at lines 3846--3847
[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
Underfull \hbox (badness 6157) in paragraph at lines 3908--3912
[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1136] [1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 4135--4137
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
Underfull \hbox (badness 2126) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1146] [1147] [1148]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1149] [1150] [1151] [1152]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1154]
[1155]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1161] [1162] [1163] [1164] [1165] [1166]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1167] [1168]
Underfull \hbox (badness 1248) in paragraph at lines 6343--6347
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6343--6347
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1169]
Underfull \hbox (badness 4647) in paragraph at lines 6498--6500
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1172]
Underfull \vbox (badness 10000) has occurred while \output is active [1173]
[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009
 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204
 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1180]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1181] [1182]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1183] [1184]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1196]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1208] [1209] [1210] [1211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1227]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1228] [1229]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1230] [1231] [1232]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 744--753
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1237] [1238]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030
 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
Underfull \hbox (badness 5388) in paragraph at lines 1145--1150
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1243]
Underfull \hbox (badness 10000) in paragraph at lines 1169--1177
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1244] [1245]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1411--1413
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1247] [1248]) (./splines-pkg.tex
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94
 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1269]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2724--2724
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2964--2964
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3173--3175
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3221--3221
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3222--3222
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3613--3613
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3891--3891
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4180--4180
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4181--4181
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4419--4419
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
Underfull \hbox (badness 3989) in paragraph at lines 4679--4686
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1332] [1333] [1334] [1335] [1336] [1337]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5064--5064
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5066--5066
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1338] [1339] [1340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5287--5287
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5305--5305
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5332--5334
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5515--5520
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5713--5713
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5880--5880
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6065--6065
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
Underfull \hbox (badness 10000) in paragraph at lines 6240--6245
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1355] [1356] [1357] [1358]
Underfull \hbox (badness 5954) in paragraph at lines 6436--6438
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
Underfull \hbox (badness 2503) in paragraph at lines 6518--6521
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6522--6524
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6525--6530
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
Underfull \hbox (badness 7238) in paragraph at lines 6561--6564
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6596--6596
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6611--6611
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1361]
[1362] [1363] [1364]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6870--6870
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7268--7272
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7367--7370
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7507
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
Underfull \hbox (badness 10000) in paragraph at lines 7914--7919
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 1210) in paragraph at lines 8269--8271
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8732--8732
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1393]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8777--8777
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8780--8780
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8918--8918
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9345--9345
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9346--9346
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9525--9527
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9986--9992
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10199--10202
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10435--10435
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10461--10466
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
Underfull \hbox (badness 4132) in paragraph at lines 10500--10504
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10554--10560
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10605--10608
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10821--10824
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10902--10906
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
Underfull \hbox (badness 10000) in paragraph at lines 10944--10950
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10982--10987
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11115--11118
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11298--11301
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11399--11399
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11432--11432
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
Underfull \hbox (badness 10000) in paragraph at lines 11445--11449
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11625--11628
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11764--11764
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11779 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11832--11832
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11844--11844
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 11897--11902
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11914--11916
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12257--12257
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12507--12509
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12530--12532
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12599--12601
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12837--12839
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12843--12847
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12843--12847
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13550--13550
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13593--13598
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13796
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1468] [1469] [1470] [1471] [1472]
Underfull \hbox (badness 1163) in paragraph at lines 14125--14133
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14245--14250
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14431--14431
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14432--14432
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14775--14775
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14776--14776
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14869--14869
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15275--15278
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15369--15369
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15994--15994
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16132--16137
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1503]
Underfull \hbox (badness 1648) in paragraph at lines 16198--16200
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16283--16283
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16841--16841
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17069--17069
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17827--17827
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17987--17987
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18081--18081
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18572--18575
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18585--18589
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18593--18597
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1541]
Underfull \hbox (badness 2042) in paragraph at lines 18651--18653
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1542]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18757--18757
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1543]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18800--18800
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18818--18818
 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 18821--18821
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18841--18841
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1544]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18844--18844
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 18879--18890
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 18879--18890
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18942--18942
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1546] [1547] [1548]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19167--19167
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1549]
Underfull \hbox (badness 1337) in paragraph at lines 19243--19246
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1550] [1551] [1552] [1553] [1554] [1555]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19562--19562
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1556]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19650--19650
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 19652--19652
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19654--19654
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1557]
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for
Underfull \hbox (badness 5260) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1558]
Underfull \hbox (badness 3049) in paragraph at lines 19739--19743
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1559] [1560] [1561]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19987--19987
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1562]
Underfull \hbox (badness 1194) in paragraph at lines 19997--20000
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1563]
Underfull \hbox (badness 1107) in paragraph at lines 20055--20057
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20110--20110
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1564]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20117--20117
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1565]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20211--20211
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1566] [1567]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20336--20336
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1568]
Underfull \hbox (badness 7740) in paragraph at lines 20399--20401
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1569]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20447--20447
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20539--20539
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20544--20544
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581]
[1582] [1583]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21398--21398
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1584]
Underfull \hbox (badness 6859) in paragraph at lines 21465--21472
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21476--21482
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595]
[1596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22214--22214
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1597] [1598] [1599] [1600] [1601]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22498--22498
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22499--22499
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1602] [1603] [1604] [1605] [1606]
Underfull \hbox (badness 1337) in paragraph at lines 22823--22829
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23388--23388
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1615] [1616]
Underfull \hbox (badness 1028) in paragraph at lines 23529--23532
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1617] [1618]
Underfull \hbox (badness 10000) in paragraph at lines 23639--23642
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1619]
Underfull \hbox (badness 7944) in paragraph at lines 23694--23696
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23756--23758
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1621] [1622]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23858--23858
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1623] [1624] [1625]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24078--24078
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1626] [1627]
Underfull \hbox (badness 10000) in paragraph at lines 24224--24227
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1628]
Underfull \hbox (badness 2134) in paragraph at lines 24276--24280
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24289--24289
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1629] [1630] [1631] [1632] [1633] [1634] [1635]
Underfull \hbox (badness 6268) in paragraph at lines 24753--24758
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24781--24781
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1637] [1638] [1639]
Underfull \hbox (badness 1867) in paragraph at lines 24958--24960
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25007--25007
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1641] [1642] [1643]
Underfull \hbox (badness 2495) in paragraph at lines 25197--25206
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1644]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25279--25279
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 25286--25288
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1645]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25373--25373
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25398--25398
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25401--25401
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1646] [1647] [1648]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25624--25624
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 25627--25633
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1649]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25673--25673
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25694--25694
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1650] [1651]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25798--25798
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1652]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25865--25865
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1653] [1654] [1655] [1656] [1657] [1658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26244--26244
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1659] [1660]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26425--26425
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26431--26431
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26440--26440
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26441--26441
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1662]
Underfull \hbox (badness 2922) in paragraph at lines 26510--26515
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26547--26547
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26550--26550
 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
[1663]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26559--26559
 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26560--26560
 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 26564--26564
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
Underfull \hbox (badness 3240) in paragraph at lines 26618--26621
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1664]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26639--26639
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26642--26642
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1665]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26725--26725
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26729--26729
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26739--26739
 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
[1666]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 26744--26744
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 26780--26786
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26802--26802
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1667]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26818--26818
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1668] [1669]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26932--26932
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1670]
Underfull \hbox (badness 2922) in paragraph at lines 26994--26999
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27032--27032
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1671]
Underfull \hbox (badness 2922) in paragraph at lines 27081--27086
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27112--27112
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
Underfull \hbox (badness 2922) in paragraph at lines 27146--27151
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1673]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27171--27171
 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27175--27175
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27195--27195
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27205--27205
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
[1674]
Underfull \hbox (badness 2922) in paragraph at lines 27240--27245
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27262--27262
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1675]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27280--27280
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
Underfull \hbox (badness 6493) in paragraph at lines 27332--27337
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27359--27359
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27361--27361
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27364--27364
 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27367--27367
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687]
[1688] [1689] [1690]
Underfull \hbox (badness 3396) in paragraph at lines 28291--28293
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1691] [1692] [1693]
Underfull \hbox (badness 2237) in paragraph at lines 28468--28470
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1694] [1695]
Underfull \hbox (badness 2591) in paragraph at lines 28632--28634
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1696]
Underfull \hbox (badness 2237) in paragraph at lines 28678--28681
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1697]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28751--28751
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1698] [1699]
Underfull \hbox (badness 3407) in paragraph at lines 28859--28863
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1700] [1701]
Underfull \hbox (badness 1337) in paragraph at lines 28992--28996
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1702] [1703] [1704] [1705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29240--29240
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29268--29268
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1706]
Underfull \hbox (badness 1616) in paragraph at lines 29294--29297
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1707]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 29373--29373
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1708]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29450--29450
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1709] [1710]
Underfull \hbox (badness 2205) in paragraph at lines 29539--29544
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30134--30134
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30135--30135
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1720] [1721] [1722] [1723] [1724]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30435--30435
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30436--30436
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1725] [1726]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 30562--30562
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30571--30571
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1727]
[1728] [1729]
Underfull \hbox (badness 1337) in paragraph at lines 30788--30792
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738]
Underfull \hbox (badness 1337) in paragraph at lines 31315--31319
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1739] [1740] [1741] [1742] [1743] [1744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 31742--31742
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1745]
Underfull \hbox (badness 6775) in paragraph at lines 31799--31804
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 31862--31862
 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1747]) (./stats4-pkg.tex [1748]
Chapter 11.
[1749] [1750] [1751]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1752] [1753] [1754]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1755] [1756] [1757])
(./tcltk-pkg.tex [1758]
Chapter 12.
[1759] [1760] [1761] [1762]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1763] [1764] [1765]
Underfull \vbox (badness 10000) has occurred while \output is active [1766]
Underfull \hbox (badness 1292) in paragraph at lines 664--671
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777]
Underfull \hbox (badness 1189) in paragraph at lines 1407--1410
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1778]) (./tools-pkg.tex
Chapter 13.
[1779]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1780]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via
Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1781]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1782]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1783]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1784] [1785] [1786] [1787] [1788] [1789] [1790]
Overfull \vbox (7.18602pt too high) has occurred while \output is active
[1791] [1792]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1793] [1794] [1795]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123
 []                              \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124
 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[] 
Underfull \hbox (badness 1112) in paragraph at lines 1139--1149
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
Underfull \hbox (badness 3724) in paragraph at lines 1139--1149
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1796]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1797]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
[1798] [1799]
Underfull \hbox (badness 10000) in paragraph at lines 1363--1366
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
[1800] [1801] [1802] [1803] [1804]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689
 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1805] [1806] [1807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1808] [1809] [1810]
[1811]
Underfull \hbox (badness 1142) in paragraph at lines 2168--2174
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
Overfull \hbox (101.58032pt too wide) in paragraph at lines 2202--2202
 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1812]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203
 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
Underfull \hbox (badness 2359) in paragraph at lines 2230--2237
[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
 and site spe-cific com-pi-la-
Underfull \hbox (badness 1102) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
Underfull \hbox (badness 4168) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
/n/10 with
[1813]
Underfull \hbox (badness 1342) in paragraph at lines 2282--2288
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1814]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358
 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1815]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404
 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430
 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1816] [1817] [1818] [1819]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2696--2696
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1820]
Underfull \hbox (badness 2486) in paragraph at lines 2741--2749
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1821] [1822] [1823] [1824] [1825]
Underfull \hbox (badness 1072) in paragraph at lines 3119--3121
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1826] [1827] [1828] [1829] [1830]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3455--3455
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1831] [1832] [1833] [1834]
Underfull \hbox (badness 4108) in paragraph at lines 3703--3710
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3803--3803
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3806--3806
 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
Underfull \hbox (badness 10000) in paragraph at lines 3823--3825
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
Underfull \hbox (badness 2932) in paragraph at lines 3840--3846
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1837] [1838]
Underfull \hbox (badness 7832) in paragraph at lines 3962--3965
[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1839]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4038--4038
 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1840]
Underfull \hbox (badness 1137) in paragraph at lines 4064--4066
[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1841] [1842] [1843]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4249--4249
 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1844] [1845]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
Underfull \hbox (badness 10000) in paragraph at lines 4422--4425
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1846]
Underfull \hbox (badness 6859) in paragraph at lines 4438--4443
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4446--4452
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
Underfull \hbox (badness 2941) in paragraph at lines 4446--4452
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1847] [1848] [1849]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4645--4645
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4646--4646
 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[] 
Underfull \hbox (badness 3240) in paragraph at lines 4658--4661
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 4662--4672
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4697--4703
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4697--4703
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1850]
Underfull \hbox (badness 1571) in paragraph at lines 4725--4729
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
Underfull \hbox (badness 2772) in paragraph at lines 4751--4756
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1851] [1852] [1853]) (./utils-pkg.tex [1854]
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1855] [1856] [1857] [1858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1859]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 382--384
[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1861]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448
 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450
 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467
 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1862] [1863]
Underfull \hbox (badness 1946) in paragraph at lines 624--628
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1864]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 680--680
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 717--723
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1865]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1866]
Underfull \hbox (badness 4505) in paragraph at lines 850--856
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1867] [1868] [1869]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1870]
Underfull \hbox (badness 1748) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1661) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1871]
Underfull \hbox (badness 10000) in paragraph at lines 1209--1212
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1872]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1881] [1882]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1883] [1884]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1885]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1886] [1887] [1888]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344
 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1889] [1890]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1891]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1892] [1893]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1894] [1895] [1896]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1897] [1898] [1899] [1900]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1901]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1902]
Underfull \hbox (badness 2452) in paragraph at lines 3359--3362
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1903] [1904] [1905] [1906] [1907] [1908]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1909] [1910]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3906--3914
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1911]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 3997--4002
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1912] [1913]
Underfull \hbox (badness 4660) in paragraph at lines 4119--4122
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1914] [1915] [1916]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1917]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1918]
Underfull \hbox (badness 1931) in paragraph at lines 4446--4453
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1919] [1920] [1921] [1922] [1923]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1924]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1925] [1926] [1927]
[1928] [1929] [1930] [1931] [1932]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1941]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1942]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1943] [1944] [1945]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1946]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6338--6341
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1947] [1948]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1949] [1950]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 5331) in paragraph at lines 6644--6650
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
[1951]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
[1952]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1953]
Underfull \hbox (badness 1314) in paragraph at lines 6877--6884
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6934--6939
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1955]
Underfull \hbox (badness 5133) in paragraph at lines 6993--6997
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7007--7010
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1956] [1957]
Underfull \hbox (badness 4132) in paragraph at lines 7174--7176
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1958] [1959] [1960]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7341--7341
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1961] [1962]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7484--7484
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1963]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7526
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1964] [1965]
Underfull \hbox (badness 10000) in paragraph at lines 7709--7711
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1859) in paragraph at lines 7937--7940
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1970]
Underfull \hbox (badness 1655) in paragraph at lines 8030--8033
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8041--8041
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8045--8045
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8053--8053
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1971] [1972]
Underfull \hbox (badness 1917) in paragraph at lines 8132--8134
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1973] [1974] [1975] [1976]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8404--8404
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8405--8405
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
Underfull \hbox (badness 10000) in paragraph at lines 8434--8436
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 8448--8450
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8456--8461
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8502--8502
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8503--8503
 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[1978] [1979]
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8632--8637
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8639--8642
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[1980] [1981]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8755--8755
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8756--8756
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8927--8927
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1984] [1985]
Underfull \hbox (badness 1789) in paragraph at lines 9058--9060
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 5203) in paragraph at lines 9631--9634
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1994] [1995] [1996]
Underfull \hbox (badness 1394) in paragraph at lines 9857--9864
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[1997]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9881--9881
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1998] [1999]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10042--10042
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2000] [2001]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10223--10223
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[2002] [2003]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10309--10309
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10312--10312
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10317--10317
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2004]
Underfull \hbox (badness 2027) in paragraph at lines 10389--10392
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2005] [2006] [2007]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10662--10662
 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10663--10663
 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2008]
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10903--10903
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2012] [2013] [2014] [2015]
Underfull \hbox (badness 10000) in paragraph at lines 11163--11167
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2016]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11181--11181
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11186--11186
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2017] [2018]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11370--11370
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2019] [2020]
Underfull \hbox (badness 1917) in paragraph at lines 11494--11497
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11494--11497
\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2021]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11517--11517
 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2022]
Underfull \hbox (badness 10000) in paragraph at lines 11580--11582
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
Underfull \hbox (badness 6725) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
Underfull \hbox (badness 6428) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2023] [2024]
Underfull \hbox (badness 3646) in paragraph at lines 11756--11758
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2025]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 11794--11794
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2026] [2027] [2028]
Underfull \hbox (badness 10000) in paragraph at lines 11975--11979
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12006--12012
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2029] [2030]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12182--12182
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
Underfull \hbox (badness 1009) in paragraph at lines 12200--12212
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2031]
Underfull \hbox (badness 2600) in paragraph at lines 12237--12239
[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2032]
Underfull \hbox (badness 1043) in paragraph at lines 12280--12285
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2033] [2034] [2035] [2036]
Underfull \hbox (badness 1888) in paragraph at lines 12573--12576
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 12588--12591
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2037]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12629--12629
 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
Underfull \hbox (badness 2158) in paragraph at lines 12684--12687
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[2038]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12732--12732
 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2039] [2040]
Underfull \hbox (badness 2302) in paragraph at lines 12889--12891
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2041] [2042]
Underfull \hbox (badness 3333) in paragraph at lines 12996--12998
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2043] [2044] [2045]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13161--13161
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
Underfull \hbox (badness 2012) in paragraph at lines 13185--13190
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
Underfull \hbox (badness 5970) in paragraph at lines 13194--13197
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13194--13197
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2046]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13249--13249
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2047]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 13280--13280
 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13287--13287
 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13289--13289
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
[2048] [2049]
Underfull \hbox (badness 10000) in paragraph at lines 13457--13459
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[2050] [2051] [2052]
Underfull \hbox (badness 6300) in paragraph at lines 13614--13621
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[2053] [2054]
Underfull \hbox (badness 2020) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2055] [2056]
Underfull \hbox (badness 5022) in paragraph at lines 13923--13927
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2057] [2058] [2059]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14094--14094
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2060] [2061] [2062] [2063] [2064] [2065]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14534--14534
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14540--14540
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Underfull \hbox (badness 4467) in paragraph at lines 14561--14563
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 14574--14578
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 1694) in paragraph at lines 14588--14592
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
Underfull \hbox (badness 1052) in paragraph at lines 14600--14602
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2066]
Underfull \hbox (badness 10000) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
Underfull \hbox (badness 1509) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
Underfull \hbox (badness 10000) in paragraph at lines 14651--14656
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 14659--14662
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2067]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14713--14713
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2068] [2069] [2070]
Underfull \hbox (badness 10000) in paragraph at lines 14915--14918
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Underfull \hbox (badness 1253) in paragraph at lines 14915--14918
[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2071]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 14931--14931
 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14998--14998
 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 15020--15020
 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2073] [2074]
Underfull \hbox (badness 1297) in paragraph at lines 15151--15153
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2075]
Underfull \hbox (badness 4036) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2076] [2077]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15335--15335
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2078]
Underfull \hbox (badness 1715) in paragraph at lines 15387--15390
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15432--15434
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2079] [2080] [2081]) [2082] [2083] [2084] (./KernSmooth-pkg.tex
Chapter 15.
[2085]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2086] [2087] [2088] [2089] [2090]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2091] [2092] [2093] [2094]) (./MASS-pkg.tex
Chapter 16.
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116]
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 6559) in paragraph at lines 2694--2697
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2133] [2134] [2135]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2136] [2137]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2138] [2139] [2140]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2141]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152]
[2153]
Underfull \hbox (badness 1845) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2154] [2155] [2156] [2157] [2158] [2159] [2160]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2161] [2162] [2163]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
[2175] [2176] [2177]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2178]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2179] [2180]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2181]
Underfull \hbox (badness 1783) in paragraph at lines 6229--6233
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2182] [2183] [2184] [2185]
Underfull \vbox (badness 10000) has occurred while \output is active [2186]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2187]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2188] [2189] [2190] [2191] [2192] [2193]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2194]
Underfull \hbox (badness 10000) in paragraph at lines 7094--7096
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7149--7155
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2196] [2197]
Underfull \hbox (badness 5091) in paragraph at lines 7328--7331
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2198] [2199]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2200]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 4686) in paragraph at lines 7961--7963
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2207] [2208]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8104--8108
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219]
[2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2229]
Underfull \hbox (badness 2035) in paragraph at lines 9595--9597
[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9610--9613
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2230]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241]
[2242] [2243]) (./Matrix-pkg.tex [2244]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
Underfull \hbox (badness 10000) in paragraph at lines 41--44
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2245]
Underfull \hbox (badness 1769) in paragraph at lines 95--98
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2246]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
Underfull \hbox (badness 1147) in paragraph at lines 159--162
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2247]
Underfull \hbox (badness 10000) in paragraph at lines 257--260
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2248] [2249]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2250]
Underfull \hbox (badness 5119) in paragraph at lines 508--512
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2251] [2252]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675
 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676
 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681
 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2253]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2254] [2255] [2256]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2257] [2258]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2259pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
Underfull \hbox (badness 2285) in paragraph at lines 1220--1225
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2260]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2261]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
Underfull \hbox (badness 2277) in paragraph at lines 1388--1391
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2262]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2264]
Underfull \hbox (badness 10000) in paragraph at lines 1531--1538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1531--1538
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1582--1588
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2265]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2266]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1710--1714
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2267] [2268]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2269] [2270] [2271] [2272] [2273]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2274]
Underfull \hbox (badness 7379) in paragraph at lines 2330--2332
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2275] [2276] [2277]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2278]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2677--2682
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2279]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2280]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2281]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3012--3016
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2284]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3528--3532
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2287]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2288] [2289]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3725--3730
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3815
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2291] [2292] [2293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2294]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2295] [2296]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2297] [2298] [2299] [2300]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534
 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537
 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2301] [2302] [2303] [2304]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2305]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2306]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2307] [2308]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130
 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131
 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134
 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2309]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2310]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
Underfull \hbox (badness 10000) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5279--5282
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2311]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2312]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2313] [2314] [2315]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2317]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5757--5762
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2318]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2319]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2320]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2321]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6096--6101
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6104--6107
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2322]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6214--6224
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2323]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2326]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6524--6530
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6545--6548
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2327]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2328] [2329]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6775--6779
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2330] [2331]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 10000) in paragraph at lines 6971--6974
Underfull \hbox (badness 10000) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2332]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7152 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2333] [2334pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 7423--7426
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7426--7431
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7426--7431
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7431--7435
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7431--7435
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7441--7442
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2335] [2336]
Underfull \hbox (badness 1009) in paragraph at lines 7577--7579
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7622--7625
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2337]
Underfull \hbox (badness 6063) in paragraph at lines 7656--7659
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2339] [2340]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2341]
Underfull \hbox (badness 2635) in paragraph at lines 7912--7917
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7912--7917
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7920--7923
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2342]
Underfull \hbox (badness 3482) in paragraph at lines 7994--8000
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2343]
Underfull \hbox (badness 1867) in paragraph at lines 8114--8116
[]\T1/ptm/m/n/10 fast sim-
[2344]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2345]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241
 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Underfull \hbox (badness 2401) in paragraph at lines 8356--8366
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2346]
Underfull \hbox (badness 3179) in paragraph at lines 8427--8430
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 8517--8520
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 8593--8596
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2349]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 8719--8721
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8721--8724
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8727--8734
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2351] [2352]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820
 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823
 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829
 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Underfull \hbox (badness 3989) in paragraph at lines 8855--8865
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8855--8865
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2353] [2354]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2355]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029
 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040
 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9044--9044
 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061
 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069
 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2356]
Underfull \hbox (badness 10000) in paragraph at lines 9122--9128
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
Underfull \hbox (badness 10000) in paragraph at lines 9139--9142
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2357]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
[2358]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9233--9233
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2359] [2360]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2361] [2362]
Underfull \hbox (badness 10000) in paragraph at lines 9550--9552
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
Underfull \hbox (badness 2351) in paragraph at lines 9556--9564
[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
Underfull \hbox (badness 1325) in paragraph at lines 9556--9564
\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
[2363] [2364]
Underfull \hbox (badness 1558) in paragraph at lines 9701--9704
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2365]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2366]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                            [2367]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9931--9931
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
Underfull \hbox (badness 1616) in paragraph at lines 9966--9978
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
Underfull \hbox (badness 10000) in paragraph at lines 9983--9986
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
Underfull \hbox (badness 10000) in paragraph at lines 9992--9999
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 10000) in paragraph at lines 10005--10015
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 4660) in paragraph at lines 10005--10015
\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2368]
Underfull \hbox (badness 6032) in paragraph at lines 10032--10036
[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
Underfull \hbox (badness 10000) in paragraph at lines 10039--10041
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
Underfull \hbox (badness 10000) in paragraph at lines 10062--10063
[]\T1/ptm/m/n/10 works via
Underfull \hbox (badness 10000) in paragraph at lines 10068--10070
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
Underfull \hbox (badness 10000) in paragraph at lines 10072--10073
[]\T1/ptm/m/n/10 all work via
Underfull \hbox (badness 10000) in paragraph at lines 10080--10083
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
[2369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10098--10098
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10102--10102
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
Underfull \hbox (badness 10000) in paragraph at lines 10123--10126
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
Underfull \hbox (badness 1648) in paragraph at lines 10151--10153
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
[2370]
Underfull \hbox (badness 10000) in paragraph at lines 10159--10162
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
Underfull \hbox (badness 2591) in paragraph at lines 10159--10162
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
Underfull \hbox (badness 10000) in paragraph at lines 10170--10174
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
Underfull \hbox (badness 2828) in paragraph at lines 10170--10174
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10181--10183
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
Underfull \hbox (badness 1158) in paragraph at lines 10199--10205
[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2372] [2373]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444
 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2374]
Underfull \hbox (badness 4621) in paragraph at lines 10485--10489
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573
 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
[2376]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2377]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638
 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2378]
Underfull \hbox (badness 10000) in paragraph at lines 10784--10788
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
[2379]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2380]
Underfull \hbox (badness 10000) in paragraph at lines 10954--10956
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2381]
Underfull \hbox (badness 5036) in paragraph at lines 11010--11012
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2382]
Underfull \hbox (badness 2970) in paragraph at lines 11143--11149
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11143--11149
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2383]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
Underfull \hbox (badness 10000) in paragraph at lines 11234--11239
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11249--11251
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2384]
Underfull \vbox (badness 10000) has occurred while \output is active [2385]
Underfull \hbox (badness 2698) in paragraph at lines 11374--11380
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2386] [2387]
Underfull \hbox (badness 10000) in paragraph at lines 11467--11469
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11485--11490
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11485--11490
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11493--11498
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2388]
Underfull \hbox (badness 2057) in paragraph at lines 11565--11567
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2389]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
[2390]
Underfull \hbox (badness 5133) in paragraph at lines 11691--11695
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11691--11695
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2391]
Underfull \hbox (badness 7649) in paragraph at lines 11798--11800
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2392] [2393] [2394]
Underfull \hbox (badness 7362) in paragraph at lines 11999--12001
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2395]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2396] [2397]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2398] [2399] [2400]) (./boot-pkg.tex
Chapter 18.
[2401] [2402] [2403] [2404] [2405] [2406] [2407]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2408]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2409] [2410] [2411]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2413]
[2414]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2415]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2420] [2421] [2422] [2423] [2424]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2425] [2426] [2427]
Underfull \vbox (badness 10000) has occurred while \output is active [2428]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2429]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2430] [2431] [2432]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2433]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2434] [2435]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2436] [2437] [2438] [2439] [2440]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2441] [2442] [2443]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2444]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2445] [2446] [2447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2448] [2449] [2450] [2451] [2452] [2453] [2454]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2455] [2456]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2457] [2458] [2459]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2460]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2461] [2462]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] [2471]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2472] [2473] [2474] [2475]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2476]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2485]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2486]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2487] [2488] [2489] [2490]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2491] [2492]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2493] [2494] [2495]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2496] [2497]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2498] [2499] [2500] [2501] [2502] [2503] [2504] [2505]) (./class-pkg.tex
[2506]
Chapter 19.
[2507] [2508] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
[2518] [2519] [2520] [2521] [2522]) (./cluster-pkg.tex
Chapter 20.
[2523]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 133--142
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 133--142
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 133--142
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2524] [2525]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2526] [2527]
Underfull \vbox (badness 10000) has occurred while \output is active [2528]
[2529]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2530] [2531]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2532]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2533] [2534]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2535]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2536]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2537]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1102--1102
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2539]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1119--1119
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1157--1157
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2540]
Underfull \hbox (badness 4144) in paragraph at lines 1189--1193
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2541]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1265--1265
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1271--1271
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2542] [2543]
Underfull \hbox (badness 10000) in paragraph at lines 1410--1415
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1458--1461
[2544]
Underfull \hbox (badness 10000) in paragraph at lines 1475--1479
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1499--1499
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1509--1509
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2545]
Underfull \hbox (badness 5741) in paragraph at lines 1549--1552
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2546]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1615--1615
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2547]
Underfull \hbox (badness 1540) in paragraph at lines 1732--1740
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2548] [2549]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1823--1823
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1842--1842
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2550] [2551] [2552] [2553]
Underfull \hbox (badness 10000) in paragraph at lines 2161--2164
Underfull \hbox (badness 3179) in paragraph at lines 2175--2181
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 2333--2336
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2557]
Underfull \hbox (badness 1292) in paragraph at lines 2401--2404
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2410--2412
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2433--2436
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2558] [2559] [2560] [2561]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2649--2649
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2562] [2563] [2564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2918--2918
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2565] [2566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3021--3021
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2567] [2568] [2569]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3217--3217
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 3285--3288
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2571]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3335--3335
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572] [2573] [2574]
Underfull \hbox (badness 10000) in paragraph at lines 3521--3524
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2575]
Underfull \hbox (badness 10000) in paragraph at lines 3584--3589
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2576]
Underfull \hbox (badness 3884) in paragraph at lines 3646--3651
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3658--3661
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 3843--3846
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3874--3877
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2580]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3927--3927
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3938--3940
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2581] [2582] [2583] [2584]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4131--4131
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4133--4133
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2585] [2586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4271--4271
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4280--4280
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4282--4282
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4285--4285
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4287--4287
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4294--4294
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2587] [2588] [2589] [2590] [2591] [2592]
Underfull \hbox (badness 10000) in paragraph at lines 4652--4658
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4668--4670
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4681--4681
 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4683--4683
 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2593]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4697--4697
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2594]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2595]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2597] [2598] [2599]) (./foreign-pkg.tex [2600]
Chapter 22.
[2601]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2602] [2603]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2604]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2605] [2606] [2607]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2608]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
Underfull \hbox (badness 6001) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2609]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2610]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2611]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658
 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2612] [2613]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2614] [2615]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2616]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2621]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2622]) (./lattice-pkg.tex
Chapter 23.
[2623] [2624] [2625]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2626]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2627] [2628] [2629] [2630]
Underfull \hbox (badness 1221) in paragraph at lines 650--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2631] [2632] [2633] [2634]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2635]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2636] [2637]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2638] [2639] [2640]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2641]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2642]
Underfull \vbox (badness 10000) has occurred while \output is active [2643]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2644]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2645] [2646] [2647] [2648]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2649]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2650] [2651] [2652]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2653] [2654] [2655] [2656] [2657]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2658] [2659]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2660]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2661] [2662]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2663]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2664] [2665] [2666] [2667]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2668]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2669] [2670] [2671] [2672] [2673]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2674]
Underfull \hbox (badness 2277) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2675] [2676]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2677]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2678] [2679]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2680] [2681] [2682] [2683] [2684] [2685]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2686] [2687]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2688] [2689]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2690] [2691] [2692] [2693] [2694] [2695]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2697]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2698]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2700] [2701]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2702] [2703]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2704] [2705]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2706] [2707]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2708]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2709] [2710]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2711]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2712] [2713] [2714] [2715] [2716] [2717]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6955--6962
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2719]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
Underfull \hbox (badness 1584) in paragraph at lines 7055--7059
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2720]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2721] [2722]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2724] [2725]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
Underfull \hbox (badness 2772) in paragraph at lines 7526--7529
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2726]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2727]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2728] [2729] [2730]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2731]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2732] [2733] [2734] [2735] [2736] [2737] [2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2740] [2741]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2742]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2743]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2744]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2745] [2746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2747] [2748]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2749]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2750] [2751] [2752] [2753] [2754] [2755] [2756]
Underfull \hbox (badness 7238) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9622--9626
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2757] [2758] [2759]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2760] [2761] [2762]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088
 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2763] [2764]) (./mgcv-pkg.tex
Chapter 24.
[2765] [2766]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2767]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152
 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2768] [2769] [2770] [2771]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2772]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408
 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2773] [2774] [2775]
Underfull \hbox (badness 2922) in paragraph at lines 607--608
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2776] [2777] [2778]
Underfull \hbox (badness 1158) in paragraph at lines 753--755
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2779]
Underfull \hbox (badness 1259) in paragraph at lines 816--817
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2780]
Underfull \vbox (badness 10000) has occurred while \output is active [2781]
[2782] [2783] [2784] [2785]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2786]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171
 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178
 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1180--1180
 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1182--1182
 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2787]
[2788]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274
 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285
 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1319--1319
 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2789]
[2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2798] [2799] [2800] [2801] [2802] [2803]
Underfull \hbox (badness 1052) in paragraph at lines 2197--2205
\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2214--2214
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Underfull \hbox (badness 1728) in paragraph at lines 2226--2229
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
Underfull \hbox (badness 1142) in paragraph at lines 2239--2243
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804]
Underfull \hbox (badness 1043) in paragraph at lines 2265--2270
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2805] [2806]
Underfull \hbox (badness 1043) in paragraph at lines 2428--2434
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2807] [2808]
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2809]
Underfull \vbox (badness 10000) has occurred while \output is active [2810]
Underfull \vbox (badness 10000) has occurred while \output is active [2811]
Underfull \vbox (badness 10000) has occurred while \output is active [2812]
[2813] [2814] [2815] [2816] [2817] [2818] [2819]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3223--3223
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2820] [2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 5189) in paragraph at lines 3584--3588
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2826] [2827]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2828]
[2829] [2830]
Underfull \hbox (badness 1184) in paragraph at lines 3870--3874
[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2831] [2832] [2833] [2834] [2835] [2836] [2837]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2838] [2839] [2840]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466
 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2841]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
[2842]
Underfull \hbox (badness 1142) in paragraph at lines 4591--4595
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2843]
Underfull \hbox (badness 10000) in paragraph at lines 4660--4669
[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2844] [2845]
Underfull \hbox (badness 5970) in paragraph at lines 4777--4783
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1418) in paragraph at lines 4777--4783
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2846]
Underfull \vbox (badness 10000) has occurred while \output is active [2847]
[2848] [2849]
Underfull \hbox (badness 1577) in paragraph at lines 5057--5060
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2850] [2851] [2852] [2853] [2854] [2855] [2856]
Underfull \hbox (badness 6708) in paragraph at lines 5453--5454
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2857]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502
 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527
 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5556--5556
 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2859]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2860] [2861] [2862] [2863] [2864] [2865]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933
 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5935--5935
 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
Underfull \hbox (badness 1142) in paragraph at lines 5956--5960
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2866] [2867] [2868] [2869] [2870] [2871]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219
 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273
 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2872] [2873] [2874] [2875]
Underfull \vbox (badness 10000) has occurred while \output is active [2876]
Underfull \vbox (badness 10000) has occurred while \output is active [2877]
[2878] [2879]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6729--6729
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888]
Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2889] [2890]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359
 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2891] [2892]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422
 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7441--7441
 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2893]
[2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904]
[2905] [2906] [2907] [2908] [2909] [2910]
Underfull \vbox (badness 10000) has occurred while \output is active [2911]
[2912]
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2913]
Underfull \hbox (badness 10000) in paragraph at lines 8717--8720
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 8717--8720
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2914] [2915] [2916]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8938--8938
 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8941--8941
 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2917] [2918] [2919]
Underfull \hbox (badness 1629) in paragraph at lines 9099--9104
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2920] [2921] [2922] [2923]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310
 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2924] [2925]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474
 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2926] [2927] [2928] [2929]
Underfull \vbox (badness 10000) has occurred while \output is active [2930]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2931]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9780--9782
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
Underfull \hbox (badness 1975) in paragraph at lines 9786--9791
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2932]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2933]
Underfull \hbox (badness 10000) in paragraph at lines 9939--9942
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
Underfull \hbox (badness 2057) in paragraph at lines 9939--9942
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2934] [2935]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2936] [2937] [2938] [2939]
Underfull \hbox (badness 1946) in paragraph at lines 10247--10254
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
Underfull \hbox (badness 2846) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2940]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2941] [2942] [2943] [2944] [2945]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637
 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[2946] [2947] [2948] [2949] [2950] [2951]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985
 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 
Underfull \hbox (badness 10000) in paragraph at lines 10998--11002
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2952]
Underfull \hbox (badness 10000) in paragraph at lines 11038--11042
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2953] [2954] [2955]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2956]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2957] [2958] [2959]
Underfull \vbox (badness 10000) has occurred while \output is active [2960]
Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2961] [2962]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703
 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727
 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732
 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2965]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738
 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739
 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2966]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[2967] [2968]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2969]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[2970] [2971] [2972]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2973] [2974] [2975] [2976]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 12468--12470
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2978] [2979]
Underfull \vbox (badness 10000) has occurred while \output is active [2980]
Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12627--12630
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 12627--12630
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2981]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 12754--12760
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2983] [2984] [2985]
Underfull \vbox (badness 10000) has occurred while \output is active [2986]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2987]
Underfull \hbox (badness 10000) in paragraph at lines 13071--13079
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2988]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2989] [2990] [2991] [2992]
Underfull \hbox (badness 3396) in paragraph at lines 13358--13361
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2993]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2994] [2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13627--13630
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
[2998]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3004]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3005] [3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3007] [3008]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019]
[3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3029] [3030] [3031] [3032] [3033]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3034] [3035] [3036]) (./nlme-pkg.tex
Chapter 25.
[3037]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3039] [3040] [3041] [3042] [3043]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3044] [3045]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3054]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3055] [3056] [3057] [3058] [3059] [3060] [3061]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3062]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3063] [3064] [3065] [3066] [3067]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3069]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3070] [3071]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091]
[3092]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3093] [3094] [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103]
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114]
[3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3117] [3118] [3119] [3120] [3121] [3122] [3123]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3133]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3134]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3136] [3137] [3138] [3139]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3140]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3141]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3142]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3143] [3144] [3145]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3146]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3147] [3148] [3149]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3150] [3151] [3152]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3153] [3154] [3155]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3164] [3165] [3166] [3167] [3168]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3169]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3170] [3171] [3172] [3173] [3174]
[3175] [3176] [3177] [3178] [3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3182]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3183] [3184] [3185] [3186]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3187]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9750--9753
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3196] [3197] [3198]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3199]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3200] [3201] [3202]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3203] [3204]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3205]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3206] [3207] [3208] [3209]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3210] [3211] [3212] [3213] [3214] [3215]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3216] [3217] [3218] [3219] [3220] [3221]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3222] [3223] [3224] [3225]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3226] [3227] [3228] [3229] [3230]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3231] [3232]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3233]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3243] [3244] [3245] [3246] [3247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3248]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3249]
Underfull \hbox (badness 1838) in paragraph at lines 13734--13741
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13734--13741
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13798--13801
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13798--13801
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13826--13829
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13826--13829
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3252]
Underfull \hbox (badness 1472) in paragraph at lines 13931--13938
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3258] [3259] [3260] [3261]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3271] [3272] [3273]
[3274] [3275] [3276] [3277] [3278] [3279] [3280]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3281] [3282] [3283]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3284] [3285] [3286] [3287] [3288]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3289]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3290] [3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3297] [3298] [3299] [3300] [3301]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3302]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
Underfull \hbox (badness 10000) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3303] [3304] [3305] [3306]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3314]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3315]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3317]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18245--18250
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 3579) in paragraph at lines 18380--18385
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3320] [3321]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18658--18667
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3333]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3334] [3335] [3336]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3338] [3339]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3340]) (./rpart-pkg.tex
Chapter 27.
[3341] [3342] [3343] [3344]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3345] [3346] [3347] [3348]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3349] [3350]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3351] [3352]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3353]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3354] [3355] [3356]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3357]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3358]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3359] [3360] [3361] [3362] [3363] [3364]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3365] [3366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3367] [3368] [3369]) (./spatial-pkg.tex [3370]
Chapter 28.
[3371] [3372] [3373] [3374] [3375] [3376]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387]
[3388] [3389]) (./survival-pkg.tex [3390]
Chapter 29.
[3391] [3392]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3393] [3394]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3395] [3396]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3397]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3398] [3399]
Underfull \vbox (badness 10000) has occurred while \output is active [3400]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3401] [3402]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3403] [3404] [3405]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3406] [3407]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3408]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                  
Underfull \vbox (badness 2698) has occurred while \output is active [3409]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271
 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3410] [3411]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3412] [3413] [3414] [3415] [3416]
Underfull \hbox (badness 1337) in paragraph at lines 1799--1803
[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854
 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3418] [3419] [3420] [3421] [3422] [3423] [3424]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351
 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3425] [3426] [3427]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3428] [3429] [3430] [3431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3432]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894
 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
Underfull \hbox (badness 1389) in paragraph at lines 2908--2910
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3433]
Underfull \hbox (badness 1048) in paragraph at lines 2963--2965
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3434]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037
 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3435] [3436]
Underfull \vbox (badness 10000) has occurred while \output is active [3437]
Underfull \vbox (badness 10000) has occurred while \output is active [3438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3439] [3440] [3441] [3442] [3443]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560
 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3444]
Underfull \vbox (badness 10000) has occurred while \output is active [3445]
[3446] [3447] [3448] [3449] [3450]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977
 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3451] [3452]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3453]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3454]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299
 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3455]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3456] [3457]
Underfull \hbox (badness 1852) in paragraph at lines 4533--4535
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3458] [3459]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669
 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3460] [3461] [3462]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3464] [3465] [3466] [3467] [3468]
Underfull \vbox (badness 2126) has occurred while \output is active [3469]
[3470] [3471]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 1043) in paragraph at lines 5560--5563
\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3472] [3473] [3474] [3475] [3476]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3477] [3478]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3479] [3480] [3481] [3482] [3483]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3484] [3485] [3486] [3487]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3488] [3489] [3490]
Underfull \hbox (badness 1253) in paragraph at lines 6915--6918
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3491] [3492]
Underfull \hbox (badness 10000) in paragraph at lines 7041--7050
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
Underfull \hbox (badness 3758) in paragraph at lines 7041--7050
\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3493]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137
 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3494]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
Underfull \hbox (badness 1038) in paragraph at lines 7197--7203
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3495]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3496]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3497] [3498] [3499]
Underfull \hbox (badness 10000) in paragraph at lines 7560--7565
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
[3500]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3501] [3502]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3503] [3504] [3505]
Underfull \hbox (badness 3058) in paragraph at lines 7969--7974
[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
Underfull \hbox (badness 7759) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
Underfull \hbox (badness 2913) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
Underfull \hbox (badness 4353) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
[3506]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3507] [3508] [3509] [3510]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3511]
Underfull \hbox (badness 1354) in paragraph at lines 8422--8426
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3512] [3513]
Underfull \hbox (badness 2035) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 8597--8604
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3514]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3515] [3516] [3517]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3518] [3519]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8965--8965
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3520] [3521] [3522] [3523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267
 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9268--9268
 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3524]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274
 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9276--9276
 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3525] [3526] [3527] [3528] [3529] [3530] [3531]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727
 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3532] [3533] [3534]) (./fullrefman.ind [3535] [3536] [3537] [3538] [3539]
[3540] [3541] [3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550]
[3551] [3552] [3553] [3554] [3555]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2205--2207
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2207--2209
[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2209--2211
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2211--2213
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2213--2215
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2215--2217
[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2217--2219
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2219--2221
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2221--2223
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2223--2225
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2225--2227
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2227--2229
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (43.3567pt too wide) in paragraph at lines 2229--2231
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2231--2233
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3556] [3557] [3558] [3559] [3560]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2771--2773
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2773--2775
[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2775--2777
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2777--2779
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2779--2781
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2781--2783
[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2783--2785
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2785--2787
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2787--2789
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2789--2791
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2791--2793
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
[3561]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2793--2795
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (43.3567pt too wide) in paragraph at lines 2795--2797
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2797--2799
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3562]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2934--2936
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3563] [3564] [3565] [3566] [3567] [3568] [3569] [3570]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3939--3941
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3941--3943
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3943--3945
[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3947--3949
[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 3949--3951
[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3951--3953
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3953--3955
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3955--3957
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3957--3959
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 3959--3961
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 3961--3963
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 3963--3965
[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3965--3967
[]\T1/pcr/m/n/10 [,Matrix,missing,missing,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3967--3969
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,index,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3969--3971
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,missing,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3971--3973
[]\T1/pcr/m/n/10 [,TsparseMatrix,missing,index,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 3975--3977
[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 3977--3979
[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 3979--3981
[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3981--3983
[]\T1/pcr/m/n/10 [,denseMatrix,index,missing,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3983--3985
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3985--3987
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3987--3989
[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3989--3991
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 3991--3993
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 3993--3995
[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 3995--3997
[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 3997--3999
[]\T1/pcr/m/n/10 [,sparseMatrix,index,index,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3999--4001
[]\T1/pcr/m/n/10 [,sparseMatrix,index,missing,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4001--4003
[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4003--4005
[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4005--4007
[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4007--4009
[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method 
[3571]
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4083--4085
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4085--4087
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4087--4089
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4089--4091
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4091--4093
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (140.8567pt too wide) in paragraph at lines 4093--4095
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4095--4097
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,lsparseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4097--4099
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4099--4101
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4101--4103
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,sparseVector-method 
Overfull \hbox (140.8567pt too wide) in paragraph at lines 4103--4105
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ndenseMatrix,missing,replValue-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4105--4107
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,nsparseMatrix,missing,replValue-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4109--4111
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4111--4113
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4113--4115
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4115--4117
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,matrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4117--4119
[]\T1/pcr/m/n/10 [<-,Matrix,ldenseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4119--4121
[]\T1/pcr/m/n/10 [<-,Matrix,lsparseMatrix,missing,replValue-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4121--4123
[]\T1/pcr/m/n/10 [<-,Matrix,matrix,missing,replValue-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4123--4125
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4125--4127
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,matrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4127--4129
[]\T1/pcr/m/n/10 [<-,Matrix,ndenseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4129--4131
[]\T1/pcr/m/n/10 [<-,Matrix,nsparseMatrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4131--4133
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4133--4135
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4135--4137
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4137--4139
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4139--4141
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4141--4143
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4143--4145
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,sparseVector-method 
[3572]
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4145--4147
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,Matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4147--4149
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4149--4151
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4151--4153
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4153--4155
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4155--4157
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,lMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4157--4159
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4159--4161
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4161--4163
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4163--4165
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,nMatrix,missing,replValue-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 4165--4167
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,index,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4167--4169
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,missing,replValue-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 4169--4171
[]\T1/pcr/m/n/10 [<-,denseMatrix,matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4171--4173
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,index,replValue-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4173--4175
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,missing,ANY-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 4175--4177
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,replValue-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4177--4179
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseMatrix-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4179--4181
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseVector-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4181--4183
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,replValue-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4183--4185
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseMatrix-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4185--4187
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4187--4189
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,matrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4189--4191
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,replValue-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4191--4193
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseMatrix-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4193--4195
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseVector-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 4195--4197
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4197--4199
[]\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4199--4201
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4201--4203
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 4203--4205
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4205--4207
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4207--4209
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4209--4211
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4211--4213
[]\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValueSp-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4213--4215
[]\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValueSp-method 
[3573]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4292--4294
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4294--4296
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4296--4298
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4300--4302
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4318--4320
[]\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method 
Underfull \vbox (badness 1824) has occurred while \output is active
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4326--4328
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4328--4330
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4330--4332
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4332--4334
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4334--4336
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dtrMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4336--4338
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4340--4342
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4342--4344
[]\T1/pcr/m/n/10 %*%,denseMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4346--4348
[]\T1/pcr/m/n/10 %*%,dgeMatrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4348--4350
[]\T1/pcr/m/n/10 %*%,dgeMatrix,dsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4356--4358
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4358--4360
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4360--4362
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,dgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4362--4364
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4364--4366
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4366--4368
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4368--4370
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4370--4372
[]\T1/pcr/m/n/10 %*%,dspMatrix,ddenseMatrix-method 
[3574]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4374--4376
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4376--4378
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4378--4380
[]\T1/pcr/m/n/10 %*%,dsyMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4384--4386
[]\T1/pcr/m/n/10 %*%,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4388--4390
[]\T1/pcr/m/n/10 %*%,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4408--4410
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4410--4412
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4412--4414
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4416--4418
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4420--4422
[]\T1/pcr/m/n/10 %*%,lgeMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4422--4424
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4424--4426
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4436--4438
[]\T1/pcr/m/n/10 %*%,matrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4460--4462
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4462--4464
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4466--4468
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4468--4470
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4472--4474
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4474--4476
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4476--4478
[]\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method 
[3575]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4490--4492
[]\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4498--4500
[]\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4506--4508
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4508--4510
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4510--4512
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4514--4516
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4516--4518
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4518--4520
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4524--4526
[]\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4526--4528
[]\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4528--4530
[]\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4532--4534
[]\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4534--4536
[]\T1/pcr/m/n/10 %%,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4536--4538
[]\T1/pcr/m/n/10 %%,ldiMatrix,ndenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4546--4548
[]\T1/pcr/m/n/10 %&%,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4552--4554
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4554--4556
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4556--4558
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,geMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4558--4560
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4560--4562
[]\T1/pcr/m/n/10 %&%,geMatrix,diagonalMatrix-method 
Underfull \vbox (badness 4328) has occurred while \output is active [3576]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4572--4574
[]\T1/pcr/m/n/10 %&%,nCsparseMatrix,nCsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4574--4576
[]\T1/pcr/m/n/10 %&%,nCsparseMatrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4580--4582
[]\T1/pcr/m/n/10 %&%,nMatrix,nsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4582--4584
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nCsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4584--4586
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4586--4588
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4590--4592
[]\T1/pcr/m/n/10 %&%,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4596--4598
[]\T1/pcr/m/n/10 %&%,sparseVector,sparseVector-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3577]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 4771--4773
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3578]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4915--4917
[]\T1/pcr/m/n/10 all.equal,abIndex,abIndex-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4917--4919
[]\T1/pcr/m/n/10 all.equal,abIndex,numLike-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4921--4923
[]\T1/pcr/m/n/10 all.equal,ANY,sparseMatrix-method 
Underfull \vbox (badness 1226) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4923--4925
[]\T1/pcr/m/n/10 all.equal,ANY,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4929--4931
[]\T1/pcr/m/n/10 all.equal,numLike,abIndex-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4931--4933
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4933--4935
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4935--4937
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4937--4939
[]\T1/pcr/m/n/10 all.equal,sparseVector,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4939--4941
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4941--4943
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseVector-method 
[3579]
Underfull \vbox (badness 1348) has occurred while \output is active
Overfull \hbox (50.8567pt too wide) in paragraph at lines 5200--5202
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5202--5204
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5204--5206
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5206--5208
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method 
[3580]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5208--5210
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5210--5212
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5216--5218
[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5222--5224
[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 5228--5230
[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5240--5242
[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5242--5244
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5244--5246
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 5246--5248
[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5248--5250
[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5254--5256
[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5256--5258
[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5258--5260
[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5264--5266
[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5276--5278
[]\T1/pcr/m/n/10 Arith,logical,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5284--5286
[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5286--5288
[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5290--5292
[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5292--5294
[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5298--5300
[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method 
Underfull \vbox (badness 4328) has occurred while \output is active [3581]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5300--5302
[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5302--5304
[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5314--5316
[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5324--5326
[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 5326--5328
[]\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5328--5330
[]\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 5330--5332
[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1824) has occurred while \output is active [3582]
Underfull \vbox (badness 1348) has occurred while \output is active [3583]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 5813--5815
[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file 
[3584]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 5975--5977
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3585] [3586] [3587]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6599--6601
[]\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6601--6603
[]\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6603--6605
[]\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6605--6607
[]\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 6609--6611
[]\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 6611--6613
[]\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6613--6615
[]\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 6615--6617
[]\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6617--6619
[]\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6619--6621
[]\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6625--6627
[]\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 6629--6631
[]\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6639--6641
[]\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3588]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6643--6645
[]\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6645--6647
[]\T1/pcr/m/n/10 cbind2,numeric,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 6647--6649
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6649--6651
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6651--6653
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6653--6655
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 6655--6657
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method 
[3589]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 6890--6892
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Underfull \vbox (badness 1019) has occurred while \output is active [3590]
[3591] [3592]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7377--7379
[]\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7379--7381
[]\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7381--7383
[]\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7387--7389
[]\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7389--7391
[]\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7393--7395
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7395--7397
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7397--7399
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lsparseMatrix-method 
Underfull \vbox (badness 2564) has occurred while \output is active
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7399--7401
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.coo-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7401--7403
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csc-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7403--7405
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csr-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7405--7407
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7407--7409
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7409--7411
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 7411--7413
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,symmetricMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7413--7415
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7415--7417
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7417--7419
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7419--7421
[]\T1/pcr/m/n/10 coerce,ddiMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7421--7423
[]\T1/pcr/m/n/10 coerce,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7423--7425
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dgeMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7425--7427
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7429--7431
[]\T1/pcr/m/n/10 coerce,ddiMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7431--7433
[]\T1/pcr/m/n/10 coerce,ddiMatrix,triangularMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7433--7435
[]\T1/pcr/m/n/10 coerce,ddiMatrix,TsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7435--7437
[]\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7437--7439
[]\T1/pcr/m/n/10 coerce,denseMatrix,generalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7439--7441
[]\T1/pcr/m/n/10 coerce,denseMatrix,RsparseMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3593]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7441--7443
[]\T1/pcr/m/n/10 coerce,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7443--7445
[]\T1/pcr/m/n/10 coerce,denseMatrix,symmetricMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7445--7447
[]\T1/pcr/m/n/10 coerce,denseMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7447--7449
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7449--7451
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7451--7453
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7453--7455
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7455--7457
[]\T1/pcr/m/n/10 coerce,dgCMatrix,lgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7459--7461
[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7461--7463
[]\T1/pcr/m/n/10 coerce,dgCMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7465--7467
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7467--7469
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7469--7471
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7471--7473
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7473--7475
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7475--7477
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7477--7479
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7479--7481
[]\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7483--7485
[]\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7485--7487
[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7487--7489
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7489--7491
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method 
Underfull \vbox (badness 2903) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7491--7493
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7493--7495
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7495--7497
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtTMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7497--7499
[]\T1/pcr/m/n/10 coerce,dgTMatrix,graphNEL-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7501--7503
[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7503--7505
[]\T1/pcr/m/n/10 coerce,dgTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7505--7507
[]\T1/pcr/m/n/10 coerce,dgTMatrix,triangularMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7507--7509
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,denseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 7509--7511
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,generalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7511--7513
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7513--7515
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 7515--7517
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7517--7519
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7523--7525
[]\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7525--7527
[]\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7531--7533
[]\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7533--7535
[]\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3594]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7539--7541
[]\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7541--7543
[]\T1/pcr/m/n/10 coerce,dsCMatrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7543--7545
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7545--7547
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7547--7549
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7549--7551
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsRMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7551--7553
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7553--7555
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsyMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7555--7557
[]\T1/pcr/m/n/10 coerce,dsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7557--7559
[]\T1/pcr/m/n/10 coerce,dsCMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7561--7563
[]\T1/pcr/m/n/10 coerce,dsCMatrix,nsCMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7565--7567
[]\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7567--7569
[]\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7569--7571
[]\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7571--7573
[]\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7573--7575
[]\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7575--7577
[]\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7579--7581
[]\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7581--7583
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7583--7585
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7585--7587
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7587--7589
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7589--7591
[]\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7593--7595
[]\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7595--7597
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7597--7599
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7599--7601
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7601--7603
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7603--7605
[]\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7607--7609
[]\T1/pcr/m/n/10 coerce,dtCMatrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7609--7611
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7611--7613
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7613--7615
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7615--7617
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7617--7619
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7619--7621
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7621--7623
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7623--7625
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ltCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7627--7629
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ntCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7629--7631
[]\T1/pcr/m/n/10 coerce,dtCMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7631--7633
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7633--7635
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7635--7637
[]\T1/pcr/m/n/10 coerce,dtpMatrix,ltpMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7639--7641
[]\T1/pcr/m/n/10 coerce,dtrMatrix,CsparseMatrix-method 
[3595]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7641--7643
[]\T1/pcr/m/n/10 coerce,dtrMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7643--7645
[]\T1/pcr/m/n/10 coerce,dtrMatrix,ltrMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7647--7649
[]\T1/pcr/m/n/10 coerce,dtrMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7649--7651
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7651--7653
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7653--7655
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7655--7657
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7657--7659
[]\T1/pcr/m/n/10 coerce,dtTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7663--7665
[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7665--7667
[]\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7669--7671
[]\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7671--7673
[]\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7673--7675
[]\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7675--7677
[]\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7677--7679
[]\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7679--7681
[]\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7683--7685
[]\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7687--7689
[]\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7691--7693
[]\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7693--7695
[]\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7697--7699
[]\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7699--7701
[]\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7705--7707
[]\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7707--7709
[]\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7709--7711
[]\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7711--7713
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7713--7715
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7715--7717
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7717--7719
[]\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7719--7721
[]\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7721--7723
[]\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7723--7725
[]\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7725--7727
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7727--7729
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7729--7731
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7731--7733
[]\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method 
[3596]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7735--7737
[]\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7737--7739
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7739--7741
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7741--7743
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7743--7745
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7745--7747
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7747--7749
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7751--7753
[]\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7753--7755
[]\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7755--7757
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7757--7759
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7759--7761
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7761--7763
[]\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7765--7767
[]\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7767--7769
[]\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7779--7781
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7781--7783
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7783--7785
[]\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7785--7787
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7787--7789
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7789--7791
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7793--7795
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7795--7797
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7797--7799
[]\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7799--7801
[]\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7801--7803
[]\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7803--7805
[]\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7805--7807
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7807--7809
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7809--7811
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7811--7813
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method 
Underfull \vbox (badness 6876) has occurred while \output is active [3597]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7815--7817
[]\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7817--7819
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7819--7821
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7823--7825
[]\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7825--7827
[]\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7827--7829
[]\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7831--7833
[]\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7833--7835
[]\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7835--7837
[]\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7837--7839
[]\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7839--7841
[]\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7841--7843
[]\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7843--7845
[]\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7845--7847
[]\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7847--7849
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7849--7851
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7851--7853
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method 
Underfull \vbox (badness 5847) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7853--7855
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7863--7865
[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7865--7867
[]\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7867--7869
[]\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7877--7879
[]\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7879--7881
[]\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3598]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7909--7911
[]\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7939--7941
[]\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7965--7967
[]\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7967--7969
[]\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7969--7971
[]\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7971--7973
[]\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7973--7975
[]\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7975--7977
[]\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7979--7981
[]\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7981--7983
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7983--7985
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7987--7989
[]\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7989--7991
[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3599]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7991--7993
[]\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7995--7997
[]\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7997--7999
[]\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7999--8001
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8001--8003
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 8005--8007
[]\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 8007--8009
[]\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8009--8011
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8011--8013
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8013--8015
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8015--8017
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8017--8019
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8019--8021
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8021--8023
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8025--8027
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8027--8029
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8031--8033
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8035--8037
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8037--8039
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8039--8041
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8041--8043
[]\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8043--8045
[]\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8047--8049
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8049--8051
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8051--8053
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8053--8055
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8055--8057
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8057--8059
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8059--8061
[]\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8061--8063
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8065--8067
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8067--8069
[]\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8069--8071
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8071--8073
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method 
[3600]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8077--8079
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8079--8081
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8081--8083
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8083--8085
[]\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8085--8087
[]\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8099--8101
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8101--8103
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8103--8105
[]\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8107--8109
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8109--8111
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8113--8115
[]\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8115--8117
[]\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8117--8119
[]\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8119--8121
[]\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8121--8123
[]\T1/pcr/m/n/10 coerce,nsparseVector,isparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8123--8125
[]\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8125--8127
[]\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8127--8129
[]\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8129--8131
[]\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8131--8133
[]\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8133--8135
[]\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8135--8137
[]\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8139--8141
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8141--8143
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8143--8145
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8145--8147
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8147--8149
[]\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8149--8151
[]\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8151--8153
[]\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8153--8155
[]\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3601]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8157--8159
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8159--8161
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8163--8165
[]\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8165--8167
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8169--8171
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8171--8173
[]\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8173--8175
[]\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8175--8177
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8177--8179
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8179--8181
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ntrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8181--8183
[]\T1/pcr/m/n/10 coerce,ntrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8183--8185
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ltrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8185--8187
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8187--8189
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ntpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8189--8191
[]\T1/pcr/m/n/10 coerce,ntTMatrix,dtTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8191--8193
[]\T1/pcr/m/n/10 coerce,ntTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8195--8197
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8197--8199
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8199--8201
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8201--8203
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8205--8207
[]\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8213--8215
[]\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8219--8221
[]\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8223--8225
[]\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8227--8229
[]\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8239--8241
[]\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8241--8243
[]\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8243--8245
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method 
[3602]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8245--8247
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8247--8249
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8249--8251
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8251--8253
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8253--8255
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8255--8257
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8257--8259
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8259--8261
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8261--8263
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8265--8267
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8271--8273
[]\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 8273--8275
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8275--8277
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 8277--8279
[]\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8281--8283
[]\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8283--8285
[]\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8285--8287
[]\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 8287--8289
[]\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8289--8291
[]\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8291--8293
[]\T1/pcr/m/n/10 coerce,sparseVector,integer-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8293--8295
[]\T1/pcr/m/n/10 coerce,sparseVector,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8295--8297
[]\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8297--8299
[]\T1/pcr/m/n/10 coerce,sparseVector,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8299--8301
[]\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8301--8303
[]\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8303--8305
[]\T1/pcr/m/n/10 coerce,sparseVector,vector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 8305--8307
[]\T1/pcr/m/n/10 coerce,table,sparseMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 8307--8309
[]\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8309--8311
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 8311--8313
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8313--8315
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8315--8317
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8317--8319
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8319--8321
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8321--8323
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8323--8325
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8325--8327
[]\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8327--8329
[]\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8329--8331
[]\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8331--8333
[]\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8333--8335
[]\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method 
[3603]
Underfull \vbox (badness 1117) has occurred while \output is active
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8471--8473
[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8477--8479
[]\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8489--8491
[]\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8491--8493
[]\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method 
[3604]
Overfull \hbox (86.8567pt too wide) in paragraph at lines 8505--8507
[]\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method 
[3605] [3606]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9034--9036
[]\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9036--9038
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9038--9040
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 9040--9042
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9042--9044
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9044--9046
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9046--9048
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9048--9050
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9050--9052
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9052--9054
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9054--9056
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dsparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9056--9058
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9058--9060
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9060--9062
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9062--9064
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9064--9066
[]\T1/pcr/m/n/10 crossprod,dgCMatrix,dgeMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9066--9068
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9068--9070
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9070--9072
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9072--9074
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9074--9076
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,numLike-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 9076--9078
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,CsparseMatrix-method 
Underfull \vbox (badness 2564) has occurred while \output is active [3607]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9078--9080
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,dgeMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 9080--9082
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9082--9084
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,lgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9084--9086
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9086--9088
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,missing-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9088--9090
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9090--9092
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,ddenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9092--9094
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,dgeMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9094--9096
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9096--9098
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9098--9100
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9100--9102
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9102--9104
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9104--9106
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9106--9108
[]\T1/pcr/m/n/10 crossprod,indMatrix,indMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9108--9110
[]\T1/pcr/m/n/10 crossprod,indMatrix,Matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9110--9112
[]\T1/pcr/m/n/10 crossprod,indMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9112--9114
[]\T1/pcr/m/n/10 crossprod,indMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9114--9116
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9116--9118
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9118--9120
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9120--9122
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9122--9124
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9124--9126
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9126--9128
[]\T1/pcr/m/n/10 crossprod,lgCMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9128--9130
[]\T1/pcr/m/n/10 crossprod,lgTMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9130--9132
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9132--9134
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9134--9136
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9140--9142
[]\T1/pcr/m/n/10 crossprod,matrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9142--9144
[]\T1/pcr/m/n/10 crossprod,matrix,dgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9144--9146
[]\T1/pcr/m/n/10 crossprod,matrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9146--9148
[]\T1/pcr/m/n/10 crossprod,matrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9158--9160
[]\T1/pcr/m/n/10 crossprod,Matrix,TsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9160--9162
[]\T1/pcr/m/n/10 crossprod,mMatrix,sparseVector-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9162--9164
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9164--9166
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9166--9168
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9168--9170
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9170--9172
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9172--9174
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9174--9176
[]\T1/pcr/m/n/10 crossprod,ngCMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9176--9178
[]\T1/pcr/m/n/10 crossprod,ngTMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9178--9180
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9180--9182
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,ndenseMatrix-method 
[3608]
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9182--9184
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9186--9188
[]\T1/pcr/m/n/10 crossprod,numLike,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9188--9190
[]\T1/pcr/m/n/10 crossprod,numLike,dgeMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9192--9194
[]\T1/pcr/m/n/10 crossprod,numLike,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 9198--9200
[]\T1/pcr/m/n/10 crossprod,pMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 9200--9202
[]\T1/pcr/m/n/10 crossprod,pMatrix,pMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9202--9204
[]\T1/pcr/m/n/10 crossprod,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9204--9206
[]\T1/pcr/m/n/10 crossprod,sparseVector,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9206--9208
[]\T1/pcr/m/n/10 crossprod,sparseVector,mMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9208--9210
[]\T1/pcr/m/n/10 crossprod,sparseVector,numLike-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9210--9212
[]\T1/pcr/m/n/10 crossprod,sparseVector,sparseVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9212--9214
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9214--9216
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9216--9218
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9218--9220
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9220--9222
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9222--9224
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9224--9226
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9258--9260
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9319--9321
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9324--9326
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3609] [3610]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 9633--9635
[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9658--9660
[]\T1/pcr/m/n/10 determinant,CHMfactor,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9660--9662
[]\T1/pcr/m/n/10 determinant,CHMfactor,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9662--9664
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9664--9666
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9666--9668
[]\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9668--9670
[]\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9670--9672
[]\T1/pcr/m/n/10 determinant,dgeMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9672--9674
[]\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9674--9676
[]\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9676--9678
[]\T1/pcr/m/n/10 determinant,dpoMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9678--9680
[]\T1/pcr/m/n/10 determinant,dppMatrix,logical-method 
Underfull \vbox (badness 1226) has occurred while \output is active
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9680--9682
[]\T1/pcr/m/n/10 determinant,dppMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9682--9684
[]\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9684--9686
[]\T1/pcr/m/n/10 determinant,dsCMatrix,missing-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9686--9688
[]\T1/pcr/m/n/10 determinant,dsparseMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9688--9690
[]\T1/pcr/m/n/10 determinant,dtCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9690--9692
[]\T1/pcr/m/n/10 determinant,dtpMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9692--9694
[]\T1/pcr/m/n/10 determinant,dtpMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9694--9696
[]\T1/pcr/m/n/10 determinant,dtrMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9696--9698
[]\T1/pcr/m/n/10 determinant,dtrMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9698--9700
[]\T1/pcr/m/n/10 determinant,indMatrix,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9700--9702
[]\T1/pcr/m/n/10 determinant,Matrix,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9702--9704
[]\T1/pcr/m/n/10 determinant,Matrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9704--9706
[]\T1/pcr/m/n/10 determinant,pMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9706--9708
[]\T1/pcr/m/n/10 determinant,sparseMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9708--9710
[]\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method 
[3611] [3612]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 10031--10033
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10101--10103
[]\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10103--10105
[]\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method 
[3613]
Underfull \vbox (badness 1117) has occurred while \output is active [3614]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 10424--10426
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3615]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10730--10732
[]\T1/pcr/m/n/10 expand,MatrixFactorization-method 
Overfull \hbox (10.01662pt too wide) in paragraph at lines 10730--10732
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
[3616]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 10927--10929
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3617] [3618]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11250--11252
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11252--11254
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11254--11256
[]\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 11256--11258
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11258--11260
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11260--11262
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11262--11264
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11264--11266
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11266--11268
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11268--11270
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11270--11272
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11272--11274
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11274--11276
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11276--11278
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11278--11280
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11280--11282
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11282--11284
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11284--11286
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11286--11288
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11288--11290
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11290--11292
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11292--11294
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11294--11296
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11296--11298
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11298--11300
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11300--11302
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11302--11304
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11304--11306
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11306--11308
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 11308--11310
[]\T1/pcr/m/n/10 forceSymmetric,matrix,ANY-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 11310--11312
[]\T1/pcr/m/n/10 forceSymmetric,Matrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11312--11314
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11314--11316
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11316--11318
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11318--11320
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11320--11322
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11322--11324
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,missing-method 
[3619]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11324--11326
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11326--11328
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11328--11330
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11330--11332
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 11332--11334
[]\T1/pcr/m/n/10 forceSymmetric,sparseMatrix,ANY-method 
[3620] [3621] [3622] [3623]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 12248--12250
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3624]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 12568--12570
[]\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class 
[3625] [3626]
Underfull \vbox (badness 5022) has occurred while \output is active [3627]
[3628]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13320--13322
[]\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13322--13324
[]\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13330--13332
[]\T1/pcr/m/n/10 is.infinite,nsparseVector-method 
[3629]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13492--13494
[]\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13498--13500
[]\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13500--13502
[]\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13566--13568
[]\T1/pcr/m/n/10 isSymmetric,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13572--13574
[]\T1/pcr/m/n/10 isSymmetric,symmetricMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13574--13576
[]\T1/pcr/m/n/10 isSymmetric,triangularMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13580--13582
[]\T1/pcr/m/n/10 isTriangular,BunchKaufman-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13584--13586
[]\T1/pcr/m/n/10 isTriangular,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13588--13590
[]\T1/pcr/m/n/10 isTriangular,diagonalMatrix-method 
[3630]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13622--13624
[]\T1/pcr/m/n/10 isTriangular,pBunchKaufman-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13626--13628
[]\T1/pcr/m/n/10 isTriangular,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13628--13630
[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13725--13727
[]\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13729--13731
[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13731--13733
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13733--13735
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13735--13737
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 13737--13739
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 13739--13741
[]\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13741--13743
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13743--13745
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method 
[3631]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13745--13747
[]\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 13749--13751
[]\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13751--13753
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 13753--13755
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 13755--13757
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 13757--13759
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method 
[3632] [3633] [3634]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14533--14535
[]\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14539--14541
[]\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 14541--14543
[]\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14543--14545
[]\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14545--14547
[]\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14547--14549
[]\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14553--14555
[]\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14563--14565
[]\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 14565--14567
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14567--14569
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14569--14571
[]\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14571--14573
[]\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14579--14581
[]\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3635]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14589--14591
[]\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14591--14593
[]\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14599--14601
[]\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14601--14603
[]\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14603--14605
[]\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 14605--14607
[]\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 14607--14609
[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method 
Underfull \vbox (badness 2035) has occurred while \output is active [3636]
[3637] [3638] [3639]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 15596--15598
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3640] [3641] [3642]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16152--16154
[]\T1/pcr/m/n/10 nonstandardGenericWithTrace-class 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16171--16173
[]\T1/pcr/m/n/10 norm,ddenseMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 16173--16175
[]\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16179--16181
[]\T1/pcr/m/n/10 norm,diagonalMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16197--16199
[]\T1/pcr/m/n/10 norm,ldenseMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16203--16205
[]\T1/pcr/m/n/10 norm,ndenseMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16205--16207
[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method 
Underfull \vbox (badness 1824) has occurred while \output is active [3643]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16457--16459
[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 16463--16465
[]\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1642) has occurred while \output is active [3644]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16475--16477
[]\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 16477--16479
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 16479--16481
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16481--16483
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 16483--16485
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16503--16505
[]\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16505--16507
[]\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16521--16523
[]\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16541--16543
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16543--16545
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method 
[3645]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16563--16565
[]\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16571--16573
[]\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16575--16577
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16577--16579
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16579--16581
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16599--16601
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16601--16603
[]\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16603--16605
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16605--16607
[]\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16609--16611
[]\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16613--16615
[]\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16617--16619
[]\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method 
[3646]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 16820--16822
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (77.3567pt too wide) in paragraph at lines 16846--16848
[]\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 
[3647]
Underfull \vbox (badness 1348) has occurred while \output is active [3648]
Underfull \vbox (badness 1117) has occurred while \output is active
Underfull \vbox (badness 1642) has occurred while \output is active [3649]
[3650] [3651] [3652]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18118--18120
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18121--18123
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18123--18125
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18125--18127
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18127--18129
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18129--18131
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (52.01662pt too wide) in paragraph at lines 18131--18133
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18133--18135
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18135--18137
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18137--18139
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (52.01662pt too wide) in paragraph at lines 18141--18143
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18143--18145
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18145--18147
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18147--18149
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18149--18151
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18151--18153
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3653] [3654]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18501--18503
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3655]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18573--18575
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Underfull \vbox (badness 1642) has occurred while \output is active [3656]
[3657]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19037--19039
[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19046--19048
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19048--19050
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19050--19052
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19052--19054
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19064--19066
[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 
[3658]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19074--19076
[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 19089--19091
[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19095--19097
[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 19211--19213
[]\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[3659]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19418--19420
[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19420--19422
[]\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19422--19424
[]\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19424--19426
[]\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method 
[3660]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 19428--19430
[]\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19430--19432
[]\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19432--19434
[]\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19434--19436
[]\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 19436--19438
[]\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19438--19440
[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19440--19442
[]\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19446--19448
[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19450--19452
[]\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19460--19462
[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19464--19466
[]\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19466--19468
[]\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19468--19470
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 19470--19472
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19472--19474
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19474--19476
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 19476--19478
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19505--19507
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19507--19509
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19509--19511
[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19511--19513
[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19515--19517
[]\T1/pcr/m/n/10 rcond,dpoMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19519--19521
[]\T1/pcr/m/n/10 rcond,dppMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19523--19525
[]\T1/pcr/m/n/10 rcond,dspMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19527--19529
[]\T1/pcr/m/n/10 rcond,dsyMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19531--19533
[]\T1/pcr/m/n/10 rcond,dtpMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19535--19537
[]\T1/pcr/m/n/10 rcond,dtrMatrix,character-method 
Underfull \vbox (badness 1348) has occurred while \output is active [3661]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19539--19541
[]\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19543--19545
[]\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19545--19547
[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method 
[3662] [3663] [3664] [3665]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20499--20501
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20501--20503
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20505--20507
[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20507--20509
[]\T1/pcr/m/n/10 Schur,generalMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20513--20515
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20515--20517
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method 
[3666]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20517--20519
[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20519--20521
[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method 
[3667]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20904--20906
[]\T1/pcr/m/n/10 show,genericFunctionWithTrace-method 
Overfull \hbox (10.01662pt too wide) in paragraph at lines 20908--20910
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20912--20914
[]\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20916--20918
[]\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method 
Underfull \vbox (badness 2564) has occurred while \output is active [3668]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20926--20928
[]\T1/pcr/m/n/10 show,refClassRepresentation-method 
[3669]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21166--21168
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21168--21170
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21171--21173
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (5.3567pt too wide) in paragraph at lines 21177--21178
[]\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21186--21188
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (5.3567pt too wide) in paragraph at lines 21191--21192
[]\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21192--21194
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (23.3567pt too wide) in paragraph at lines 21195--21199
[]\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21200--21202
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21248--21250
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3670]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21281--21283
[]\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 21283--21285
[]\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21285--21287
[]\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21295--21297
[]\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21297--21299
[]\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 21299--21301
[]\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 21301--21303
[]\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21305--21307
[]\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21307--21309
[]\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21313--21315
[]\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21319--21321
[]\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method 
Underfull \vbox (badness 2035) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21321--21323
[]\T1/pcr/m/n/10 solve,diagonalMatrix,Matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21323--21325
[]\T1/pcr/m/n/10 solve,diagonalMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21325--21327
[]\T1/pcr/m/n/10 solve,diagonalMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21327--21329
[]\T1/pcr/m/n/10 solve,dpoMatrix,dgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21333--21335
[]\T1/pcr/m/n/10 solve,dppMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21341--21343
[]\T1/pcr/m/n/10 solve,dsCMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21343--21345
[]\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21345--21347
[]\T1/pcr/m/n/10 solve,dsCMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21353--21355
[]\T1/pcr/m/n/10 solve,dspMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21359--21361
[]\T1/pcr/m/n/10 solve,dsyMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21361--21363
[]\T1/pcr/m/n/10 solve,dsyMatrix,denseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21367--21369
[]\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21369--21371
[]\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method 
[3671]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21377--21379
[]\T1/pcr/m/n/10 solve,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21383--21385
[]\T1/pcr/m/n/10 solve,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21395--21397
[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21407--21409
[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21409--21411
[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 21411--21413
[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 21413--21415
[]\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21425--21427
[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method 
[3672]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 21573--21575
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3673] [3674]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22011--22013
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22013--22015
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22015--22017
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings 
[3675] [3676] [3677] [3678]
Underfull \vbox (badness 5022) has occurred while \output is active [3679]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22879--22881
[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22881--22883
[]\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 22883--22885
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 22885--22887
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 22887--22889
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22889--22891
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22891--22893
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22893--22895
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 22895--22897
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22897--22899
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22899--22901
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22901--22903
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dtrMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22903--22905
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22905--22907
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,lsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22907--22909
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22909--22911
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22911--22913
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22913--22915
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22915--22917
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 22917--22919
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22919--22921
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22921--22923
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22923--22925
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 22925--22927
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 22927--22929
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22929--22931
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22931--22933
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 22933--22935
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22935--22937
[]\T1/pcr/m/n/10 tcrossprod,dtrMatrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22937--22939
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,indMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22939--22941
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22941--22943
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22943--22945
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22945--22947
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22947--22949
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22949--22951
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22951--22953
[]\T1/pcr/m/n/10 tcrossprod,lgCMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 22953--22955
[]\T1/pcr/m/n/10 tcrossprod,lgeMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22955--22957
[]\T1/pcr/m/n/10 tcrossprod,lgTMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22957--22959
[]\T1/pcr/m/n/10 tcrossprod,lsparseMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22961--22963
[]\T1/pcr/m/n/10 tcrossprod,matrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22963--22965
[]\T1/pcr/m/n/10 tcrossprod,matrix,dgeMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22965--22967
[]\T1/pcr/m/n/10 tcrossprod,matrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22967--22969
[]\T1/pcr/m/n/10 tcrossprod,matrix,dsCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22969--22971
[]\T1/pcr/m/n/10 tcrossprod,matrix,dtrMatrix-method 
[3680]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22971--22973
[]\T1/pcr/m/n/10 tcrossprod,Matrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22973--22975
[]\T1/pcr/m/n/10 tcrossprod,matrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22975--22977
[]\T1/pcr/m/n/10 tcrossprod,matrix,lsCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22983--22985
[]\T1/pcr/m/n/10 tcrossprod,Matrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22985--22987
[]\T1/pcr/m/n/10 tcrossprod,matrix,nsCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22987--22989
[]\T1/pcr/m/n/10 tcrossprod,Matrix,numLike-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22989--22991
[]\T1/pcr/m/n/10 tcrossprod,Matrix,pMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22991--22993
[]\T1/pcr/m/n/10 tcrossprod,matrix,pMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22993--22995
[]\T1/pcr/m/n/10 tcrossprod,Matrix,symmetricMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22995--22997
[]\T1/pcr/m/n/10 tcrossprod,Matrix,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22997--22999
[]\T1/pcr/m/n/10 tcrossprod,mMatrix,sparseVector-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22999--23001
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23001--23003
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 23003--23005
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23005--23007
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23007--23009
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23009--23011
[]\T1/pcr/m/n/10 tcrossprod,ngCMatrix,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23011--23013
[]\T1/pcr/m/n/10 tcrossprod,ngTMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23013--23015
[]\T1/pcr/m/n/10 tcrossprod,nsparseMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23015--23017
[]\T1/pcr/m/n/10 tcrossprod,numLike,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23017--23019
[]\T1/pcr/m/n/10 tcrossprod,numLike,dgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 23019--23021
[]\T1/pcr/m/n/10 tcrossprod,numLike,Matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23021--23023
[]\T1/pcr/m/n/10 tcrossprod,numLike,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 23023--23025
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,missing-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 23025--23027
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,pMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 23027--23029
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23029--23031
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,sparseVector-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23031--23033
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23033--23035
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,mMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23035--23037
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,numLike-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23037--23039
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23039--23041
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseVector-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23041--23043
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23043--23045
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,Matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23045--23047
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,missing-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 23047--23049
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,TsparseMatrix-method 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 23090--23092
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 tensor.prod.model.matrix\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3681] [3682] [3683] [3684]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 23729--23731
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3685] [3686] [3687]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 24388--24390
[]\T1/pcr/m/n/10 updown,character,mMatrix,CHMfactor-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 24390--24392
[]\T1/pcr/m/n/10 updown,logical,mMatrix,CHMfactor-method 
[3688] [3689]
Underfull \vbox (badness 2285) has occurred while \output is active [3690]
[3691] [3692]) (./fullrefman.aux)
Package rerunfilecheck Warning: File `fullrefman.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.
 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts
/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/c
ourier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmri8a.pfb>
Output written on fullrefman.pdf (3743 pages, 10275608 bytes).
Transcript written on fullrefman.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo
aded.
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.
) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./fullrefman.out) (./fullrefman.out)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texliv
e/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4]
[5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20]
[21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49]) [50]
[1] [2] (./base-pkg.tex
Chapter 1.
[3] [4]
Underfull \hbox (badness 6741) in paragraph at lines 135--141
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 .
Underfull \hbox (badness 4805) in paragraph at lines 135--141
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10
 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is
Underfull \hbox (badness 4316) in paragraph at lines 135--141
\T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-
wise, it is \T1/pcr/m/n/10 (double.base ^
Underfull \hbox (badness 5050) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It
Underfull \hbox (badness 1028) in paragraph at lines 141--149
\T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/pcr/m/n/10 double.base
Underfull \hbox (badness 2980) in paragraph at lines 141--149
\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 141--149
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As
Underfull \hbox (badness 1668) in paragraph at lines 152--159
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5] [6] [7]
Underfull \hbox (badness 10000) in paragraph at lines 339--342
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8] [9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 534--540
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13]
[14] [15]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
Underfull \hbox (badness 1838) in paragraph at lines 1178--1181
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[21] [22] [23] [24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670
 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
Underfull \hbox (badness 1303) in paragraph at lines 1698--1701
[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[28] [29]
Underfull \hbox (badness 10000) in paragraph at lines 1816--1818
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[30] [31]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
Underfull \hbox (badness 10000) in paragraph at lines 1991--1993
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[32] [33] [34] [35]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[38]
Underfull \hbox (badness 1107) in paragraph at lines 2460--2462
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326
 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327
 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334
 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335
 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012
 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
Underfull \hbox (badness 4927) in paragraph at lines 4267--4271
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 4267--4271
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
Underfull \hbox (badness 1199) in paragraph at lines 4596--4602
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
Underfull \hbox (badness 2573) in paragraph at lines 4607--4610
[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[70] [71]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4766--4766
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[72] [73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5019--5021
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5416--5424
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[82] [83] [84] [85] [86] [87] [88] [89]
Underfull \hbox (badness 1796) in paragraph at lines 5979--5987
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[90] [91] [92]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6175--6175
 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6176--6176
 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6311--6315
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
Underfull \hbox (badness 1635) in paragraph at lines 6353--6356
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6357--6360
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[95]
Underfull \hbox (badness 1308) in paragraph at lines 6388--6396
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[96] [97]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6542--6542
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6584--6586
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6732--6735
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6732--6735
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[101] [102]
Underfull \hbox (badness 1406) in paragraph at lines 6914--6920
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 6914--6920
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 6934--6936
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
Underfull \hbox (badness 1067) in paragraph at lines 6976--6983
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7168--7168
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
Underfull \hbox (badness 1231) in paragraph at lines 7293--7299
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7506
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7649--7649
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7887--7887
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
Underfull \hbox (badness 8132) in paragraph at lines 7988--7992
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7988--7992
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 8007--8017
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8007--8017
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[119]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8039--8043
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[120] [121] [122] [123] [124] [125]
Underfull \hbox (badness 1629) in paragraph at lines 8525--8537
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8525--8537
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8788
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
Underfull \hbox (badness 10000) in paragraph at lines 8972--8976
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[132] [133]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9063--9063
 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9065--9065
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9090--9090
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9091--9091
 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
Underfull \hbox (badness 5403) in paragraph at lines 9209--9211
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[136] [137] [138]
Underfull \hbox (badness 1603) in paragraph at lines 9439--9442
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10045--10050
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10100--10100
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10101--10101
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
Underfull \hbox (badness 1168) in paragraph at lines 10203--10208
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[150]
Underfull \hbox (badness 10000) in paragraph at lines 10242--10248
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10249--10252
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[151] [152]
Underfull \hbox (badness 2828) in paragraph at lines 10408--10412
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10408--10412
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10441--10441
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10514--10514
 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[155] [156]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10658--10658
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
Underfull \hbox (badness 6396) in paragraph at lines 10847--10855
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
Underfull \hbox (badness 10000) in paragraph at lines 10856--10858
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11073--11076
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[163] [164] [165] [166] [167] [168] [169] [170] [171]
Underfull \hbox (badness 5288) in paragraph at lines 11771--11773
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
Underfull \hbox (badness 3039) in paragraph at lines 11781--11786
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 10000) in paragraph at lines 11841--11843
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
Underfull \hbox (badness 4569) in paragraph at lines 11963--11967
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 11963--11967
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12078--12080
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12919--12919
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 2221) in paragraph at lines 13365--13374
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13365--13374
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13626--13628
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
Underfull \hbox (badness 2573) in paragraph at lines 13741--13743
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13891--13893
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14004
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14011--14014
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 14032--14032
 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 14055--14055
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
Underfull \hbox (badness 10000) in paragraph at lines 14147--14150
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14157--14157
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
Underfull \hbox (badness 10000) in paragraph at lines 14223--14226
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14240--14240
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 1472) in paragraph at lines 14293--14300
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14293--14300
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14301--14305
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[208] [209] [210]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14464--14464
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14465--14465
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14695--14695
 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 14698--14698
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
Underfull \hbox (badness 1168) in paragraph at lines 14782--14786
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 14782--14786
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
Underfull \hbox (badness 6944) in paragraph at lines 14880--14883
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[216]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14905--14905
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
Underfull \hbox (badness 10000) in paragraph at lines 15043--15045
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15063--15063
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15069--15069
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
Underfull \hbox (badness 2790) in paragraph at lines 15076--15079
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 1024) in paragraph at lines 15107--15111
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[220]
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
[]\T1/ptm/m/n/10 The im-ple-men-ta-tion has \T1/pcr/m/n/10 formatC() \T1/ptm/m/
n/10 call-ing \T1/pcr/m/n/10 prettyNum()
Underfull \hbox (badness 10000) in paragraph at lines 15170--15173
\T1/ptm/m/n/10 (only if \T1/pcr/m/n/10 zero.print \T1/ptm/m/n/10 is not \T1/pcr
/m/n/10 NULL\T1/ptm/m/n/10 ) which it-self calls
Underfull \hbox (badness 2818) in paragraph at lines 15192--15194
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15198--15202
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15203--15211
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[221] [222]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15304--15304
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15326--15326
 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16143--16143
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[235] [236]
Underfull \hbox (badness 2418) in paragraph at lines 16252--16256
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16259--16262
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 16294--16301
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[237] [238] [239] [240]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16540--16540
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16565--16572
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[241] [242] [243] [244]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16834--16834
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16863--16863
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [245]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16914--16914
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[246] [247] [248] [249] [250]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17279--17279
 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[251] [252] [253] [254]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17533--17533
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257]
Underfull \hbox (badness 2435) in paragraph at lines 17796--17798
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[258]
Underfull \hbox (badness 2285) in paragraph at lines 17862--17864
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17870--17870
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[259]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17880--17880
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 17900--17900
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 18040--18040
 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18043--18043
 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18049--18049
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[262] [263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 18176--18176
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18184--18184
 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[264] [265] [266]
Underfull \hbox (badness 10000) in paragraph at lines 18389--18391
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[267]
Underfull \hbox (badness 4217) in paragraph at lines 18473--18482
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18488--18504
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[268] [269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18907--18910
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[275] [276]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19030--19030
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19165--19167
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 19214--19214
 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19215--19215
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1975) in paragraph at lines 19793--19796
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[288] [289] [290] [291] [292] [293]
Underfull \hbox (badness 1077) in paragraph at lines 20188--20193
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[294]
Underfull \hbox (badness 10000) in paragraph at lines 20202--20209
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20276--20280
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20425--20429
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 20425--20429
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20430--20437
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
[298] [299]
Underfull \hbox (badness 10000) in paragraph at lines 20561--20568
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[300]
Underfull \hbox (badness 10000) in paragraph at lines 20682--20686
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[301]
Underfull \hbox (badness 5161) in paragraph at lines 20752--20757
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20752--20757
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[302] [303] [304]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20919--20919
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20923--20923
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[305]
Underfull \hbox (badness 3343) in paragraph at lines 20979--20983
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[306]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21065--21065
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21076--21076
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[307] [308]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21187--21187
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21190--21190
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
Underfull \hbox (badness 6380) in paragraph at lines 21235--21240
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[309] [310]
Underfull \hbox (badness 2564) in paragraph at lines 21326--21329
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21356--21356
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[311] [312]
Underfull \hbox (badness 1400) in paragraph at lines 21524--21528
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[313] [314] [315]
Underfull \hbox (badness 2469) in paragraph at lines 21694--21700
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
Underfull \hbox (badness 4531) in paragraph at lines 21694--21700
\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[316] [317] [318] [319] [320] [321] [322] [323] [324]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22321--22321
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22322--22322
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 22325--22325
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[325] [326]
Underfull \hbox (badness 1655) in paragraph at lines 22449--22453
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[327] [328] [329] [330]
Underfull \hbox (badness 2277) in paragraph at lines 22698--22701
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[331] [332] [333] [334] [335] [336] [337] [338]
Underfull \hbox (badness 1484) in paragraph at lines 23263--23271
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 23263--23271
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[339] [340]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23340--23340
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[341] [342] [343] [344] [345] [346] [347]
Underfull \hbox (badness 1448) in paragraph at lines 23845--23853
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[348] [349]
Underfull \hbox (badness 3849) in paragraph at lines 23959--23964
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[350]
Underfull \hbox (badness 7308) in paragraph at lines 24036--24042
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 10000) in paragraph at lines 24036--24042
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 1210) in paragraph at lines 24036--24042
[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24046--24049
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[351] [352]
Underfull \hbox (badness 10000) in paragraph at lines 24199--24201
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[353] [354] [355]
Underfull \hbox (badness 6188) in paragraph at lines 24418--24421
[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 2197) in paragraph at lines 24902--24906
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 24902--24906
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[363]
Underfull \hbox (badness 2846) in paragraph at lines 24916--24920
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
Underfull \hbox (badness 1990) in paragraph at lines 24916--24920
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24958--24958
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24962--24962
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[364]
Underfull \hbox (badness 10000) in paragraph at lines 25010--25016
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25010--25016
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 25023--25025
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25074--25074
 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[366] [367] [368]
Underfull \hbox (badness 8189) in paragraph at lines 25267--25273
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[369] [370] [371]
Underfull \hbox (badness 1694) in paragraph at lines 25489--25492
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[372] [373] [374]
Underfull \hbox (badness 1603) in paragraph at lines 25736--25738
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[375] [376]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25863--25871
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[377] [378]
Underfull \hbox (badness 3271) in paragraph at lines 26070--26073
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[379] [380] [381]
Underfull \hbox (badness 3138) in paragraph at lines 26370--26376
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 26370--26376
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[382]
Underfull \hbox (badness 1194) in paragraph at lines 26383--26386
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 1389) in paragraph at lines 26409--26411
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 26429--26435
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 26444--26449
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Underfull \hbox (badness 1009) in paragraph at lines 26462--26465
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[383]
Underfull \hbox (badness 10000) in paragraph at lines 26478--26481
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-
Underfull \hbox (badness 10000) in paragraph at lines 26486--26491
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 26500--26507
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 26500--26507
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[384] [385] [386] [387]
Underfull \vbox (badness 10000) has occurred while \output is active [388]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26844--26844
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 26857--26861
\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[389] [390]
Underfull \hbox (badness 10000) in paragraph at lines 27004--27007
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
Underfull \hbox (badness 1062) in paragraph at lines 27004--27007
\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[391] [392] [393]
Underfull \hbox (badness 10000) in paragraph at lines 27273--27279
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 27273--27279
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
[394]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27295--27295
 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27307--27307
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[395] [396] [397] [398] [399] [400] [401]
Underfull \hbox (badness 1817) in paragraph at lines 27741--27745
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[402]
Underfull \hbox (badness 1796) in paragraph at lines 27809--27812
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[403] [404] [405]
Underfull \hbox (badness 10000) in paragraph at lines 28009--28012
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[406] [407] [408] [409] [410] [411] [412] [413] [414] [415]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28686--28686
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[416] [417] [418] [419]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28952--28952
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28963--28963
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28969--28969
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28970--28970
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28973--28973
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[420]
Underfull \hbox (badness 7415) in paragraph at lines 29048--29052
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[421]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29069--29069
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 29115--29115
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[422] [423]
Underfull \hbox (badness 3713) in paragraph at lines 29238--29249
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[424]
Underfull \hbox (badness 1248) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
Underfull \hbox (badness 10000) in paragraph at lines 29382--29389
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[425] [426]
Underfull \hbox (badness 1533) in paragraph at lines 29500--29503
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[427] [428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29645--29645
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29663--29674
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[430] [431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29807--29807
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29809--29809
 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29810--29810
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29811--29811
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29812--29812
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29819--29819
 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[432] [433] [434] [435] [436] [437]
Underfull \hbox (badness 4048) in paragraph at lines 30166--30171
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
Underfull \hbox (badness 1824) in paragraph at lines 30166--30171
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[438] [439] [440] [441] [442] [443] [444] [445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30707--30707
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 7558) in paragraph at lines 31209--31213
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31219--31221
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
[452]
Underfull \hbox (badness 5417) in paragraph at lines 31224--31227
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31228--31230
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31231--31233
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31636--31640
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31980--31980
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31983--31983
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32367--32367
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[470] [471] [472] [473] [474] [475]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32802--32802
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[476]
Underfull \hbox (badness 1158) in paragraph at lines 32906--32911
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[477]
Underfull \hbox (badness 10000) in paragraph at lines 32933--32939
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1762) in paragraph at lines 32933--32939
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[478] [479]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33091--33091
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[480] [481] [482]
Underfull \hbox (badness 8151) in paragraph at lines 33351--33354
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[483] [484] [485] [486]
Underfull \hbox (badness 1210) in paragraph at lines 33586--33588
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498]
[499] [500]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34523--34523
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[501] [502] [503]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34775--34775
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34777--34777
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[504]
Underfull \hbox (badness 4954) in paragraph at lines 34820--34826
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 34820--34826
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[505] [506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34931--34931
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35259--35259
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
[511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35274--35274
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[512] [513] [514] [515] [516] [517]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35715--35715
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35716--35716
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[518] [519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35980--35980
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
Underfull \hbox (badness 6110) in paragraph at lines 36064--36074
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 36064--36074
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 36064--36074
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36108--36114
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1460) in paragraph at lines 36120--36127
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 36120--36127
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[523] [524] [525] [526]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 36397--36397
 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[527] [528] [529] [530] [531] [532] [533] [534]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36959--36959
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[535] [536] [537] [538]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 37207--37207
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[539]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37251--37251
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[540] [541] [542] [543] [544] [545]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37685--37685
 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 37688--37688
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[546]
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 37739--37746
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[547]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37792--37792
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[548] [549] [550] [551]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38093--38093
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[552]
Underfull \vbox (badness 7777) has occurred while \output is active [553]
[554]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38258--38258
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38296--38296
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
Underfull \hbox (badness 4792) in paragraph at lines 38345--38350
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 38345--38350
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[556]
Underfull \hbox (badness 2452) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 38435--38438
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[557] [558] [559]
Underfull \hbox (badness 10000) in paragraph at lines 38623--38627
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 38638--38641
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[560] [561]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38770--38770
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[562]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38840--38840
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[563] [564] [565]
Underfull \hbox (badness 1082) in paragraph at lines 38984--38987
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[566] [567]
Underfull \hbox (badness 1038) in paragraph at lines 39175--39178
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[568] [569] [570] [571] [572] [573]
Underfull \hbox (badness 1442) in paragraph at lines 39538--39542
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[574] [575] [576]
Underfull \hbox (badness 4096) in paragraph at lines 39784--39787
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[577] [578]
Underfull \hbox (badness 7888) in paragraph at lines 39898--39902
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[579] [580]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40052--40052
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40054--40054
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
[581]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40056--40056
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 40069--40071
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[582]
Underfull \hbox (badness 10000) in paragraph at lines 40149--40152
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[583] [584]
Underfull \hbox (badness 3872) in paragraph at lines 40267--40270
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[585]
Underfull \hbox (badness 5475) in paragraph at lines 40333--40337
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 10000) in paragraph at lines 40751--40758
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40807--40816
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40807--40816
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40817--40825
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 2503) in paragraph at lines 40817--40825
\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[592]
Underfull \hbox (badness 1337) in paragraph at lines 40883--40891
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40892--40895
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[593]
Underfull \hbox (badness 3460) in paragraph at lines 40946--40949
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 40950--40952
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40959--40959
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[594] [595] [596]
Underfull \hbox (badness 10000) in paragraph at lines 41176--41178
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[597] [598]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41298--41298
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41300--41300
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [599]
[600] [601] [602] [603]
Underfull \hbox (badness 6542) in paragraph at lines 41662--41664
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[604] [605]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41781--41781
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[606]
Underfull \hbox (badness 1708) in paragraph at lines 41849--41857
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 41849--41857
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 4859) in paragraph at lines 41879--41884
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[607]
Underfull \hbox (badness 3895) in paragraph at lines 41941--41953
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 41941--41953
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[608] [609] [610] [611] [612]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 42264--42264
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[613] [614] [615] [616] [617] [618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42731--42731
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[619]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42740--42740
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[620]
Underfull \hbox (badness 1803) in paragraph at lines 42865--42868
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
[621]
Underfull \hbox (badness 3471) in paragraph at lines 42869--42876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[622] [623] [624]
Underfull \hbox (badness 3668) in paragraph at lines 43084--43086
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[625]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 43188--43188
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[626]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43263--43263
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 43271--43271
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[627] [628]
Underfull \hbox (badness 6220) in paragraph at lines 43401--43406
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 43401--43406
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
[629]
Underfull \hbox (badness 10000) in paragraph at lines 43422--43427
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
Underfull \hbox (badness 4229) in paragraph at lines 43422--43427
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[630]
Underfull \hbox (badness 2818) in paragraph at lines 43512--43518
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[631]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 43547--43547
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[632]
Underfull \hbox (badness 1622) in paragraph at lines 43641--43643
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[633] [634] [635] [636] [637]
Underfull \hbox (badness 2846) in paragraph at lines 44004--44008
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44044--44044
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
Underfull \hbox (badness 3209) in paragraph at lines 44065--44069
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[639]) (./compiler-pkg.tex [640]
Chapter 2.
[641]
Underfull \hbox (badness 2884) in paragraph at lines 105--119
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 105--119
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
Underfull \vbox (badness 1033) has occurred while \output is active [651]
[652] [653] [654] [655]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 702--705
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[660] [661]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1146--1149
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1544
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1541--1544
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[669] [670] [671]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1730--1733
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681] [682] [683] [684] [685] [686]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[688]
Underfull \vbox (badness 1789) has occurred while \output is active [689]
[690]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[691] [692]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[704]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
Underfull \hbox (badness 10000) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[725] [726]
Underfull \hbox (badness 10000) in paragraph at lines 379--387
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
Underfull \hbox (badness 1748) in paragraph at lines 379--387
\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[727] [728]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[738] [739]
Underfull \hbox (badness 10000) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
Underfull \hbox (badness 1173) in paragraph at lines 1322--1325
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[741] [742] [743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1565) in paragraph at lines 1810--1815
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1810--1815
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[749]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
Underfull \hbox (badness 1184) in paragraph at lines 1934--1944
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 1934--1944
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[750] [751]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[752] [753]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
Underfull \hbox (badness 2326) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
Underfull \hbox (badness 2318) in paragraph at lines 2341--2351
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
Underfull \hbox (badness 2460) in paragraph at lines 2341--2351
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
Underfull \hbox (badness 1221) in paragraph at lines 2341--2351
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[756] [757]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
Underfull \vbox (badness 10000) has occurred while \output is active [758]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560
 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561
 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829
Underfull \vbox (badness 10000) has occurred while \output is active [764]
[765] [766] [767] [768]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161
 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3246--3246
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
Underfull \hbox (badness 1264) in paragraph at lines 3384--3389
\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[772] [773] [774]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545
 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
Underfull \hbox (badness 8170) in paragraph at lines 3571--3574
[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[775]
Underfull \hbox (badness 10000) in paragraph at lines 3655--3659
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space&
oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
Underfull \hbox (badness 5260) in paragraph at lines 3785--3788
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
Underfull \hbox (badness 5939) in paragraph at lines 4113--4118
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
Underfull \hbox (badness 3612) in paragraph at lines 4514--4519
\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
Underfull \hbox (badness 1348) in paragraph at lines 4828--4831
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[793]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
Underfull \hbox (badness 7522) in paragraph at lines 4892--4898
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[794]
Underfull \hbox (badness 1112) in paragraph at lines 4923--4927
[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[795]
Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[796] [797] [798]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
Underfull \hbox (badness 7397) in paragraph at lines 5256--5260
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[799] [800]
Underfull \hbox (badness 1552) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5390--5392
[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5422--5428
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[801]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[802] [803]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
Underfull \hbox (badness 10000) in paragraph at lines 5747--5749
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[807] [808] [809] [810] [811]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458
 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465
 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 6728--6733
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1803) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6728--6733
\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[822]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833
 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
Underfull \hbox (badness 5954) in paragraph at lines 6872--6875
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https :
[824]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
Underfull \hbox (badness 10000) in paragraph at lines 7084--7091
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7084--7091
\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[827]
Underfull \hbox (badness 5607) in paragraph at lines 7168--7172
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
Underfull \hbox (badness 5637) in paragraph at lines 7345--7351
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
[830]
Underfull \hbox (badness 1721) in paragraph at lines 7378--7381
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[831] [832]
Underfull \hbox (badness 1231) in paragraph at lines 7546--7548
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.
Underfull \hbox (badness 4647) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[837] [838] [839]
Underfull \hbox (badness 3792) in paragraph at lines 177--180
[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[840]
Underfull \hbox (badness 1412) in paragraph at lines 287--292
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[844] [845]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846] [847]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 694--698
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[848]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[849]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818
 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[850] [851]
Underfull \hbox (badness 10000) in paragraph at lines 960--964
[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977
 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979
 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855] [856] [857] [858]
Underfull \hbox (badness 1024) in paragraph at lines 1425--1433
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1459--1461
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1530--1530
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1536--1536
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1537--1537
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
Underfull \hbox (badness 10000) in paragraph at lines 1837--1843
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[865]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1874--1874
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1883--1883
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1968--1968
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2097--2097
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2102--2102
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2376--2376
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
Underfull \hbox (badness 1009) in paragraph at lines 2388--2395
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[874]
Underfull \hbox (badness 7273) in paragraph at lines 2470--2474
[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2483--2483
 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
Underfull \hbox (badness 1226) in paragraph at lines 2878--2882
\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2931--2931
 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[882]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2935--2935
 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
Underfull \hbox (badness 10000) in paragraph at lines 2987--2990
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[883] [884] [885]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3192--3192
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3197--3197
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3336--3341
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3522--3522
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3541--3541
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[891]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3545--3545
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[892] [893]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3722--3722
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3723--3723
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3762--3762
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [895]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3814--3814
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3822--3822
 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3832--3832
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
Underfull \hbox (badness 10000) in paragraph at lines 3895--3899
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[897] [898]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4006--4006
 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[899] [900] [901]
Underfull \hbox (badness 3930) in paragraph at lines 4213--4215
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[902] [903] [904] [905] [906]
Underfull \hbox (badness 1286) in paragraph at lines 4524--4527
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[907]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4629--4629
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4634--4634
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[908]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4678--4678
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
Underfull \hbox (badness 1264) in paragraph at lines 4752--4765
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[910] [911]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4895
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[912]
Underfull \hbox (badness 10000) in paragraph at lines 5020--5023
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf, id=2988
2, 289.08pt x 289.08pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"mai.pdf>
[913 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 5081--5083
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf, id=2989
5, 259.97125pt x 332.24126pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [914]
[915 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/oma.pdf>]
[916]
Underfull \hbox (badness 10000) in paragraph at lines 5271--5273
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[917]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5327--5327
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5328--5328
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5693--5693
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5694--5694
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
Underfull \hbox (badness 1360) in paragraph at lines 5745--5749
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[924] [925] [926] [927] [928] [929] [930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6179--6179
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6185--6185
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
Underfull \hbox (badness 10000) in paragraph at lines 6612--6614
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
Underfull \hbox (badness 1028) in paragraph at lines 6706--6708
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
<"/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf, id=3031
0, 361.35pt x 50.1875pt>
<use "/builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/"pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750
[][] 
[939 </builddir/build/BUILD/R-3.6.0/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6843--6843
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6874--6874
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [941]
[942]
Underfull \hbox (badness 10000) in paragraph at lines 6996--6998
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7023--7023
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7029--7029
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
Underfull \hbox (badness 2600) in paragraph at lines 7089--7091
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[944] [945] [946] [947]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7321--7321
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7708--7708
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7712--7712
 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7724--7724
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[955] [956] [957] [958] [959]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8073--8073
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8076--8076
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8080--8080
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8251--8251
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8252--8252
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[963] [964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8356--8356
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
Underfull \hbox (badness 2080) in paragraph at lines 8367--8372
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[965]
Underfull \hbox (badness 1112) in paragraph at lines 8415--8419
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[966]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8475--8475
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8490--8490
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8621--8621
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8806--8806
 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[971]
Underfull \hbox (badness 10000) in paragraph at lines 8834--8836
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
Underfull \hbox (badness 1584) in paragraph at lines 8868--8874
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8916 \HeaderA{units}{Graphical Units}{units}
                                               [973]
Underfull \hbox (badness 1205) in paragraph at lines 8981--8983
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 9100--9100
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
Underfull \hbox (badness 10000) in paragraph at lines 476--482
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
Underfull \hbox (badness 1024) in paragraph at lines 476--482
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[985] [986] [987] [988] [989] [990] [991] [992] [993] [994]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
Underfull \hbox (badness 1430) in paragraph at lines 1166--1171
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[995] [996] [997] [998]
Underfull \hbox (badness 3219) in paragraph at lines 1380--1383
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[999] [1000] [1001] [1002] [1003] [1004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1982--1982
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1983--1983
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
Underfull \hbox (badness 2961) in paragraph at lines 2018--2023
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1009]
Underfull \hbox (badness 1430) in paragraph at lines 2077--2082
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
Underfull \hbox (badness 4479) in paragraph at lines 2106--2109
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[1010] [1011] [1012]
Underfull \hbox (badness 2894) in paragraph at lines 2313--2320
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[1013] [1014] [1015]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
Underfull \hbox (badness 1430) in paragraph at lines 2481--2486
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1016]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540
 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
[1019]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1020] [1021] [1022]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1023] [1024] [1025] [1026] [1027]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028] [1029]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
Underfull \hbox (badness 2799) in paragraph at lines 3411--3417
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1030] [1031]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1035]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747
 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046]
[1047]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1048]
Underfull \hbox (badness 1430) in paragraph at lines 4532--4537
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1049] [1050] [1051]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061]
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
Underfull \hbox (badness 6859) in paragraph at lines 6056--6062
[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
Underfull \hbox (badness 10000) in paragraph at lines 6056--6062
\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1072] [1073] [1074] [1075] [1076]
Underfull \hbox (badness 1867) in paragraph at lines 6366--6368
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1077]
Underfull \hbox (badness 10000) in paragraph at lines 6403--6409
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1078] [1079]
Underfull \hbox (badness 1371) in paragraph at lines 6535--6538
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
[1080] [1081] [1082]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1087] [1088] [1089]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1090] [1091]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558
 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568
 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619
 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1093]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637
 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640
 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657
 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672
 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
Underfull \vbox (badness 10000) has occurred while \output is active [1094]
[1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105]
[1106] [1107] [1108]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1111] [1112] [1113]
Underfull \hbox (badness 1478) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
[1114] [1115]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360
 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
Underfull \hbox (badness 1194) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1119]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
Underfull \hbox (badness 10000) in paragraph at lines 3403--3408
[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
Underfull \hbox (badness 6268) in paragraph at lines 3403--3408
\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1130] [1131]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1132]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651
[]
[1133] [1134]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
Underfull \hbox (badness 10000) in paragraph at lines 3809--3810
[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
Underfull \hbox (badness 10000) in paragraph at lines 3846--3847
[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
Underfull \hbox (badness 6157) in paragraph at lines 3908--3912
[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1136] [1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 4135--4137
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
Underfull \hbox (badness 2126) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1146] [1147] [1148]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1149] [1150] [1151] [1152]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1154]
[1155]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1161] [1162] [1163] [1164] [1165] [1166]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1167] [1168]
Underfull \hbox (badness 1248) in paragraph at lines 6343--6347
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6343--6347
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1169]
Underfull \hbox (badness 4647) in paragraph at lines 6498--6500
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1172]
Underfull \vbox (badness 10000) has occurred while \output is active [1173]
[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009
 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204
 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1180]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1181] [1182]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1183] [1184]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1196]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1208] [1209] [1210] [1211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1227]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1228] [1229]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1230] [1231] [1232]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 744--753
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1237] [1238]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030
 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
Underfull \hbox (badness 5388) in paragraph at lines 1145--1150
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1243]
Underfull \hbox (badness 10000) in paragraph at lines 1169--1177
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1244] [1245]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1411--1413
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1247] [1248]) (./splines-pkg.tex
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94
 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1269]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1536--1540
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2724--2724
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2964--2964
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3173--3175
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3221--3221
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3222--3222
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3613--3613
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3891--3891
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4180--4180
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4181--4181
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4419--4419
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
Underfull \hbox (badness 3989) in paragraph at lines 4679--4686
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1332] [1333] [1334] [1335] [1336] [1337]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5064--5064
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5066--5066
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1338] [1339] [1340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5287--5287
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5305--5305
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5332--5334
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5515--5520
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5515--5520
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5713--5713
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5880--5880
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6065--6065
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6173--6173
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
Underfull \hbox (badness 10000) in paragraph at lines 6240--6245
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1355] [1356] [1357] [1358]
Underfull \hbox (badness 5954) in paragraph at lines 6436--6438
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
Underfull \hbox (badness 2503) in paragraph at lines 6518--6521
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6522--6524
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6525--6530
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
Underfull \hbox (badness 7238) in paragraph at lines 6561--6564
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6596--6596
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6611--6611
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1361]
[1362] [1363] [1364]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6870--6870
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7268--7272
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7367--7370
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7504--7507
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
Underfull \hbox (badness 10000) in paragraph at lines 7914--7919
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 1210) in paragraph at lines 8269--8271
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8732--8732
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1393]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8777--8777
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8780--8780
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8918--8918
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9345--9345
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9346--9346
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9525--9527
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9986--9992
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10199--10202
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10435--10435
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10461--10466
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
Underfull \hbox (badness 4132) in paragraph at lines 10500--10504
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10554--10560
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10605--10608
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10821--10824
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10902--10906
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
Underfull \hbox (badness 10000) in paragraph at lines 10944--10950
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10982--10987
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11115--11118
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11298--11301
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11399--11399
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11432--11432
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
Underfull \hbox (badness 10000) in paragraph at lines 11445--11449
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11625--11628
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11764--11764
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11779 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11832--11832
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11844--11844
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 11897--11902
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11914--11916
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12257--12257
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12507--12509
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12530--12532
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12599--12601
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12837--12839
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12843--12847
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12843--12847
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13550--13550
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13593--13598
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13792--13796
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1468] [1469] [1470] [1471] [1472]
Underfull \hbox (badness 1163) in paragraph at lines 14125--14133
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14245--14250
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14431--14431
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14432--14432
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14775--14775
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14776--14776
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14869--14869
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15275--15278
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15369--15369
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15994--15994
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16132--16137
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1503]
Underfull \hbox (badness 1648) in paragraph at lines 16198--16200
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16213--16222
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16283--16283
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16841--16841
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17069--17069
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17827--17827
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17987--17987
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18034--18034
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18081--18081
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18572--18575
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18585--18589
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18593--18597
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1541]
Underfull \hbox (badness 2042) in paragraph at lines 18651--18653
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1542]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18757--18757
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1543]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18800--18800
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18818--18818
 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 18821--18821
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18841--18841
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1544]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18844--18844
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 18879--18890
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 18879--18890
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18942--18942
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1546] [1547] [1548]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19167--19167
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1549]
Underfull \hbox (badness 1337) in paragraph at lines 19243--19246
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1550] [1551] [1552] [1553] [1554] [1555]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19562--19562
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1556]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19650--19650
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 19652--19652
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19654--19654
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1557]
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for
Underfull \hbox (badness 5260) in paragraph at lines 19700--19704
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1558]
Underfull \hbox (badness 3049) in paragraph at lines 19739--19743
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1559] [1560] [1561]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19987--19987
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1562]
Underfull \hbox (badness 1194) in paragraph at lines 19997--20000
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1563]
Underfull \hbox (badness 1107) in paragraph at lines 20055--20057
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20110--20110
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1564]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20117--20117
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1565]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20211--20211
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1566] [1567]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20336--20336
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1568]
Underfull \hbox (badness 7740) in paragraph at lines 20399--20401
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1569]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20447--20447
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20539--20539
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20544--20544
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581]
[1582] [1583]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21398--21398
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1584]
Underfull \hbox (badness 6859) in paragraph at lines 21465--21472
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21476--21482
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595]
[1596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22214--22214
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1597] [1598] [1599] [1600] [1601]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22498--22498
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22499--22499
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1602] [1603] [1604] [1605] [1606]
Underfull \hbox (badness 1337) in paragraph at lines 22823--22829
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23388--23388
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1615] [1616]
Underfull \hbox (badness 1028) in paragraph at lines 23529--23532
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1617] [1618]
Underfull \hbox (badness 10000) in paragraph at lines 23639--23642
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1619]
Underfull \hbox (badness 7944) in paragraph at lines 23694--23696
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23756--23758
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1621] [1622]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23858--23858
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1623] [1624] [1625]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24078--24078
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1626] [1627]
Underfull \hbox (badness 10000) in paragraph at lines 24224--24227
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1628]
Underfull \hbox (badness 2134) in paragraph at lines 24276--24280
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24289--24289
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1629] [1630] [1631] [1632] [1633] [1634] [1635]
Underfull \hbox (badness 6268) in paragraph at lines 24753--24758
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24781--24781
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1637] [1638] [1639]
Underfull \hbox (badness 1867) in paragraph at lines 24958--24960
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 24971--24975
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25007--25007
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1641] [1642] [1643]
Underfull \hbox (badness 2495) in paragraph at lines 25197--25206
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1644]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25279--25279
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 25286--25288
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1645]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25373--25373
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25398--25398
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25401--25401
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1646] [1647] [1648]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25624--25624
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 25627--25633
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1649]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25673--25673
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25694--25694
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1650] [1651]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25798--25798
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1652]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25865--25865
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1653] [1654] [1655] [1656] [1657] [1658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26244--26244
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1659] [1660]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26425--26425
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26431--26431
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26440--26440
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26441--26441
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1662]
Underfull \hbox (badness 2922) in paragraph at lines 26510--26515
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26547--26547
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26550--26550
 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
[1663]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26559--26559
 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26560--26560
 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 26564--26564
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
Underfull \hbox (badness 3240) in paragraph at lines 26618--26621
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1664]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26639--26639
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26642--26642
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1665]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26725--26725
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26729--26729
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26739--26739
 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
[1666]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 26744--26744
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 26780--26786
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26802--26802
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1667]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26818--26818
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1668] [1669]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26932--26932
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1670]
Underfull \hbox (badness 2922) in paragraph at lines 26994--26999
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27032--27032
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1671]
Underfull \hbox (badness 2922) in paragraph at lines 27081--27086
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27112--27112
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
Underfull \hbox (badness 2922) in paragraph at lines 27146--27151
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1673]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27171--27171
 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27175--27175
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27195--27195
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27205--27205
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
[1674]
Underfull \hbox (badness 2922) in paragraph at lines 27240--27245
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27262--27262
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1675]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27280--27280
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
Underfull \hbox (badness 6493) in paragraph at lines 27332--27337
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27359--27359
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27361--27361
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27364--27364
 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27367--27367
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687]
[1688] [1689] [1690]
Underfull \hbox (badness 3396) in paragraph at lines 28291--28293
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1691] [1692] [1693]
Underfull \hbox (badness 2237) in paragraph at lines 28468--28470
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1694] [1695]
Underfull \hbox (badness 2591) in paragraph at lines 28632--28634
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1696]
Underfull \hbox (badness 2237) in paragraph at lines 28678--28681
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1697]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28751--28751
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1698] [1699]
Underfull \hbox (badness 3407) in paragraph at lines 28859--28863
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1700] [1701]
Underfull \hbox (badness 1337) in paragraph at lines 28992--28996
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1702] [1703] [1704] [1705]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29240--29240
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29268--29268
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1706]
Underfull \hbox (badness 1616) in paragraph at lines 29294--29297
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1707]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 29373--29373
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1708]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29450--29450
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1709] [1710]
Underfull \hbox (badness 2205) in paragraph at lines 29539--29544
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30134--30134
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30135--30135
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1720] [1721] [1722] [1723] [1724]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30435--30435
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30436--30436
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1725] [1726]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 30562--30562
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30571--30571
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1727]
[1728] [1729]
Underfull \hbox (badness 1337) in paragraph at lines 30788--30792
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738]
Underfull \hbox (badness 1337) in paragraph at lines 31315--31319
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1739] [1740] [1741] [1742] [1743] [1744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 31742--31742
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1745]
Underfull \hbox (badness 6775) in paragraph at lines 31799--31804
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 31862--31862
 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1747]) (./stats4-pkg.tex [1748]
Chapter 11.
[1749] [1750] [1751]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1752] [1753] [1754]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1755] [1756] [1757])
(./tcltk-pkg.tex [1758]
Chapter 12.
[1759] [1760] [1761] [1762]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1763] [1764] [1765]
Underfull \vbox (badness 10000) has occurred while \output is active [1766]
Underfull \hbox (badness 1292) in paragraph at lines 664--671
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777]
Underfull \hbox (badness 1189) in paragraph at lines 1407--1410
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1778]) (./tools-pkg.tex
Chapter 13.
[1779]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1780]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via
Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1781]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1782]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1783]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1784] [1785] [1786] [1787] [1788] [1789] [1790]
Overfull \vbox (7.18602pt too high) has occurred while \output is active
[1791] [1792]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1793] [1794] [1795]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123
 []                              \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124
 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[] 
Underfull \hbox (badness 1112) in paragraph at lines 1139--1149
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
Underfull \hbox (badness 3724) in paragraph at lines 1139--1149
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1796]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1797]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
[1798] [1799]
Underfull \hbox (badness 10000) in paragraph at lines 1363--1366
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
[1800] [1801] [1802] [1803] [1804]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689
 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1805] [1806] [1807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1808] [1809] [1810]
[1811]
Underfull \hbox (badness 1142) in paragraph at lines 2168--2174
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
Overfull \hbox (101.58032pt too wide) in paragraph at lines 2202--2202
 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1812]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203
 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
Underfull \hbox (badness 2359) in paragraph at lines 2230--2237
[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
 and site spe-cific com-pi-la-
Underfull \hbox (badness 1102) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
Underfull \hbox (badness 4168) in paragraph at lines 2230--2237
\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
/n/10 with
[1813]
Underfull \hbox (badness 1342) in paragraph at lines 2282--2288
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1814]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358
 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1815]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404
 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430
 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1816] [1817] [1818] [1819]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2696--2696
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1820]
Underfull \hbox (badness 2486) in paragraph at lines 2741--2749
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1821] [1822] [1823] [1824] [1825]
Underfull \hbox (badness 1072) in paragraph at lines 3119--3121
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1826] [1827] [1828] [1829] [1830]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3455--3455
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1831] [1832] [1833] [1834]
Underfull \hbox (badness 4108) in paragraph at lines 3703--3710
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3803--3803
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3806--3806
 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
Underfull \hbox (badness 10000) in paragraph at lines 3823--3825
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
Underfull \hbox (badness 2932) in paragraph at lines 3840--3846
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1837] [1838]
Underfull \hbox (badness 7832) in paragraph at lines 3962--3965
[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1839]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4038--4038
 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1840]
Underfull \hbox (badness 1137) in paragraph at lines 4064--4066
[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1841] [1842] [1843]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4249--4249
 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1844] [1845]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
Underfull \hbox (badness 10000) in paragraph at lines 4422--4425
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1846]
Underfull \hbox (badness 6859) in paragraph at lines 4438--4443
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4446--4452
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
Underfull \hbox (badness 2941) in paragraph at lines 4446--4452
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1847] [1848] [1849]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4645--4645
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4646--4646
 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[] 
Underfull \hbox (badness 3240) in paragraph at lines 4658--4661
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 4662--4672
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4697--4703
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4697--4703
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1850]
Underfull \hbox (badness 1571) in paragraph at lines 4725--4729
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
Underfull \hbox (badness 2772) in paragraph at lines 4751--4756
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1851] [1852] [1853]) (./utils-pkg.tex [1854]
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1855] [1856] [1857] [1858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1859]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 382--384
[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1861]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448
 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450
 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467
 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1862] [1863]
Underfull \hbox (badness 1946) in paragraph at lines 624--628
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1864]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 680--680
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 717--723
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1865]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1866]
Underfull \hbox (badness 4505) in paragraph at lines 850--856
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1867] [1868] [1869]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1870]
Underfull \hbox (badness 1748) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1661) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1871]
Underfull \hbox (badness 10000) in paragraph at lines 1209--1212
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1872]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1881] [1882]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1883] [1884]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1885]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1886] [1887] [1888]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344
 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1889] [1890]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1891]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1892] [1893]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1894] [1895] [1896]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1897] [1898] [1899] [1900]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1901]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1902]
Underfull \hbox (badness 2452) in paragraph at lines 3359--3362
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1903] [1904] [1905] [1906] [1907] [1908]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1909] [1910]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3906--3914
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1911]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 3997--4002
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 3997--4002
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1912] [1913]
Underfull \hbox (badness 4660) in paragraph at lines 4119--4122
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1914] [1915] [1916]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1917]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1918]
Underfull \hbox (badness 1931) in paragraph at lines 4446--4453
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1919] [1920] [1921] [1922] [1923]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1924]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1925] [1926] [1927]
[1928] [1929] [1930] [1931] [1932]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1941]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1942]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1943] [1944] [1945]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1946]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6338--6341
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1947] [1948]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1949] [1950]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 5331) in paragraph at lines 6644--6650
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
[1951]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
[1952]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1953]
Underfull \hbox (badness 1314) in paragraph at lines 6877--6884
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6934--6939
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1955]
Underfull \hbox (badness 5133) in paragraph at lines 6993--6997
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7007--7010
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1956] [1957]
Underfull \hbox (badness 4132) in paragraph at lines 7174--7176
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1958] [1959] [1960]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7341--7341
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1961] [1962]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7484--7484
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1963]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7526
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1964] [1965]
Underfull \hbox (badness 10000) in paragraph at lines 7709--7711
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1859) in paragraph at lines 7937--7940
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1970]
Underfull \hbox (badness 1655) in paragraph at lines 8030--8033
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8041--8041
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8045--8045
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8053--8053
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1971] [1972]
Underfull \hbox (badness 1917) in paragraph at lines 8132--8134
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1973] [1974] [1975] [1976]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8404--8404
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8405--8405
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
Underfull \hbox (badness 10000) in paragraph at lines 8434--8436
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 8448--8450
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8456--8461
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8502--8502
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8503--8503
 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[1978] [1979]
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8632--8637
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8632--8637
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8639--8642
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[1980] [1981]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8755--8755
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8756--8756
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8927--8927
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1984] [1985]
Underfull \hbox (badness 1789) in paragraph at lines 9058--9060
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 5203) in paragraph at lines 9631--9634
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1994] [1995] [1996]
Underfull \hbox (badness 1394) in paragraph at lines 9857--9864
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[1997]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9881--9881
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1998] [1999]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10042--10042
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2000] [2001]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10223--10223
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[2002] [2003]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10309--10309
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10312--10312
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10317--10317
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2004]
Underfull \hbox (badness 2027) in paragraph at lines 10389--10392
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2005] [2006] [2007]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10662--10662
 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10663--10663
 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2008]
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10670--10675
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10903--10903
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2012] [2013] [2014] [2015]
Underfull \hbox (badness 10000) in paragraph at lines 11163--11167
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2016]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11181--11181
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11186--11186
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2017] [2018]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11370--11370
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2019] [2020]
Underfull \hbox (badness 1917) in paragraph at lines 11494--11497
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11494--11497
\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2021]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11517--11517
 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2022]
Underfull \hbox (badness 10000) in paragraph at lines 11580--11582
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
Underfull \hbox (badness 6725) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
Underfull \hbox (badness 6428) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11630--11639
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11630--11639
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2023] [2024]
Underfull \hbox (badness 3646) in paragraph at lines 11756--11758
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2025]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 11794--11794
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2026] [2027] [2028]
Underfull \hbox (badness 10000) in paragraph at lines 11975--11979
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12006--12012
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2029] [2030]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12182--12182
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
Underfull \hbox (badness 1009) in paragraph at lines 12200--12212
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2031]
Underfull \hbox (badness 2600) in paragraph at lines 12237--12239
[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2032]
Underfull \hbox (badness 1043) in paragraph at lines 12280--12285
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2033] [2034] [2035] [2036]
Underfull \hbox (badness 1888) in paragraph at lines 12573--12576
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 12588--12591
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2037]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12629--12629
 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
Underfull \hbox (badness 2158) in paragraph at lines 12684--12687
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[2038]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12732--12732
 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2039] [2040]
Underfull \hbox (badness 2302) in paragraph at lines 12889--12891
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2041] [2042]
Underfull \hbox (badness 3333) in paragraph at lines 12996--12998
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2043] [2044] [2045]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13161--13161
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
Underfull \hbox (badness 2012) in paragraph at lines 13185--13190
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
Underfull \hbox (badness 5970) in paragraph at lines 13194--13197
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13194--13197
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2046]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13249--13249
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2047]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 13280--13280
 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13287--13287
 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13289--13289
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
[2048] [2049]
Underfull \hbox (badness 10000) in paragraph at lines 13457--13459
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[2050] [2051] [2052]
Underfull \hbox (badness 6300) in paragraph at lines 13614--13621
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 13614--13621
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[2053] [2054]
Underfull \hbox (badness 2020) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 13783--13799
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2055] [2056]
Underfull \hbox (badness 5022) in paragraph at lines 13923--13927
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 13930--13933
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2057] [2058] [2059]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14094--14094
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2060] [2061] [2062] [2063] [2064] [2065]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14534--14534
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14540--14540
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Underfull \hbox (badness 4467) in paragraph at lines 14561--14563
[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 14574--14578
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 1694) in paragraph at lines 14588--14592
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14594--14599
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
Underfull \hbox (badness 1052) in paragraph at lines 14600--14602
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2066]
Underfull \hbox (badness 10000) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
Underfull \hbox (badness 1509) in paragraph at lines 14630--14635
\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
Underfull \hbox (badness 10000) in paragraph at lines 14651--14656
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 14659--14662
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2067]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14713--14713
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2068] [2069] [2070]
Underfull \hbox (badness 10000) in paragraph at lines 14915--14918
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Underfull \hbox (badness 1253) in paragraph at lines 14915--14918
[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2071]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 14931--14931
 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14998--14998
 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 15020--15020
 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2073] [2074]
Underfull \hbox (badness 1297) in paragraph at lines 15151--15153
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2075]
Underfull \hbox (badness 4036) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2076] [2077]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15335--15335
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2078]
Underfull \hbox (badness 1715) in paragraph at lines 15387--15390
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15432--15434
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2079] [2080] [2081]) [2082] [2083] [2084] (./KernSmooth-pkg.tex
Chapter 15.
[2085]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2086] [2087] [2088] [2089] [2090]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2091] [2092] [2093] [2094]) (./MASS-pkg.tex
Chapter 16.
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116]
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 6559) in paragraph at lines 2694--2697
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2133] [2134] [2135]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2136] [2137]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2138] [2139] [2140]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2141]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152]
[2153]
Underfull \hbox (badness 1845) in paragraph at lines 4143--4145
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2154] [2155] [2156] [2157] [2158] [2159] [2160]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2161] [2162] [2163]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
[2175] [2176] [2177]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2178]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2179] [2180]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2181]
Underfull \hbox (badness 1783) in paragraph at lines 6229--6233
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2182] [2183] [2184] [2185]
Underfull \vbox (badness 10000) has occurred while \output is active [2186]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2187]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2188] [2189] [2190] [2191] [2192] [2193]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2194]
Underfull \hbox (badness 10000) in paragraph at lines 7094--7096
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7149--7155
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2196] [2197]
Underfull \hbox (badness 5091) in paragraph at lines 7328--7331
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2198] [2199]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2200]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 4686) in paragraph at lines 7961--7963
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2207] [2208]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8104--8108
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219]
[2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2229]
Underfull \hbox (badness 2035) in paragraph at lines 9595--9597
[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9610--9613
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2230]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241]
[2242] [2243]) (./Matrix-pkg.tex [2244]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
Underfull \hbox (badness 10000) in paragraph at lines 41--44
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2245]
Underfull \hbox (badness 1769) in paragraph at lines 95--98
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2246]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
Underfull \hbox (badness 1147) in paragraph at lines 159--162
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2247]
Underfull \hbox (badness 10000) in paragraph at lines 257--260
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2248] [2249]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2250]
Underfull \hbox (badness 5119) in paragraph at lines 508--512
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2251] [2252]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675
 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676
 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681
 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2253]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2254] [2255] [2256]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2257] [2258]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2259pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
Underfull \hbox (badness 2285) in paragraph at lines 1220--1225
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2260]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2261]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
Underfull \hbox (badness 2277) in paragraph at lines 1388--1391
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2262]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2263]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2264]
Underfull \hbox (badness 10000) in paragraph at lines 1531--1538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1531--1538
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1582--1588
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2265]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2266]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1710--1714
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2267] [2268]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2269] [2270] [2271] [2272] [2273]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2274]
Underfull \hbox (badness 7379) in paragraph at lines 2330--2332
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2275] [2276] [2277]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2278]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2677--2682
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2677--2682
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2279]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2713--2718
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2280]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2281]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3012--3016
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2284]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3528--3532
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2287]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2288] [2289]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3725--3730
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3815
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2291] [2292] [2293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2294]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2295] [2296]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2297] [2298] [2299] [2300]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534
 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537
 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2301] [2302] [2303] [2304]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2305]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2306]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2307] [2308]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130
 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131
 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134
 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2309]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2310]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
Underfull \hbox (badness 10000) in paragraph at lines 5277--5279
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5279--5282
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2311]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2312]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2313] [2314] [2315]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2317]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5757--5762
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2318]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2319]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2320]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2321]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6096--6101
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6104--6107
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2322]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6214--6224
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2323]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2326]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6524--6530
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6545--6548
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2327]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2328] [2329]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6775--6779
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2330] [2331]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 10000) in paragraph at lines 6971--6974
Underfull \hbox (badness 10000) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2332]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7152 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2333] [2334pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 7423--7426
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7426--7431
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7426--7431
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7431--7435
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7431--7435
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7441--7442
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2335] [2336]
Underfull \hbox (badness 1009) in paragraph at lines 7577--7579
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7622--7625
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2337]
Underfull \hbox (badness 6063) in paragraph at lines 7656--7659
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2339] [2340]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2341]
Underfull \hbox (badness 2635) in paragraph at lines 7912--7917
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7912--7917
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7920--7923
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2342]
Underfull \hbox (badness 3482) in paragraph at lines 7994--8000
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2343]
Underfull \hbox (badness 1867) in paragraph at lines 8114--8116
[]\T1/ptm/m/n/10 fast sim-
[2344]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2345]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241
 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Underfull \hbox (badness 2401) in paragraph at lines 8356--8366
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2346]
Underfull \hbox (badness 3179) in paragraph at lines 8427--8430
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 8517--8520
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 8593--8596
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2349]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 8719--8721
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8721--8724
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8727--8734
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2351] [2352]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820
 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823
 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829
 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Underfull \hbox (badness 3989) in paragraph at lines 8855--8865
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8855--8865
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2353] [2354]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2355]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029
 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040
 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9044--9044
 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061
 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069
 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2356]
Underfull \hbox (badness 10000) in paragraph at lines 9122--9128
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
Underfull \hbox (badness 10000) in paragraph at lines 9139--9142
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2357]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
[2358]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9233--9233
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2359] [2360]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2361] [2362]
Underfull \hbox (badness 10000) in paragraph at lines 9550--9552
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
Underfull \hbox (badness 2351) in paragraph at lines 9556--9564
[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
Underfull \hbox (badness 1325) in paragraph at lines 9556--9564
\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
[2363] [2364]
Underfull \hbox (badness 1558) in paragraph at lines 9701--9704
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2365]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2366]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                            [2367]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9931--9931
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
Underfull \hbox (badness 1616) in paragraph at lines 9966--9978
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
Underfull \hbox (badness 10000) in paragraph at lines 9983--9986
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
Underfull \hbox (badness 10000) in paragraph at lines 9992--9999
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 10000) in paragraph at lines 10005--10015
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
Underfull \hbox (badness 4660) in paragraph at lines 10005--10015
\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2368]
Underfull \hbox (badness 6032) in paragraph at lines 10032--10036
[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
Underfull \hbox (badness 10000) in paragraph at lines 10039--10041
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
Underfull \hbox (badness 10000) in paragraph at lines 10062--10063
[]\T1/ptm/m/n/10 works via
Underfull \hbox (badness 10000) in paragraph at lines 10068--10070
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
Underfull \hbox (badness 10000) in paragraph at lines 10072--10073
[]\T1/ptm/m/n/10 all work via
Underfull \hbox (badness 10000) in paragraph at lines 10080--10083
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
[2369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10098--10098
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10102--10102
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
Underfull \hbox (badness 10000) in paragraph at lines 10123--10126
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
Underfull \hbox (badness 1648) in paragraph at lines 10151--10153
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
[2370]
Underfull \hbox (badness 10000) in paragraph at lines 10159--10162
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
Underfull \hbox (badness 2591) in paragraph at lines 10159--10162
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
Underfull \hbox (badness 10000) in paragraph at lines 10170--10174
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
Underfull \hbox (badness 2828) in paragraph at lines 10170--10174
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
Underfull \hbox (badness 6592) in paragraph at lines 10181--10183
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
Underfull \hbox (badness 1158) in paragraph at lines 10199--10205
[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2372] [2373]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444
 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2374]
Underfull \hbox (badness 4621) in paragraph at lines 10485--10489
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573
 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
[2376]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2377]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638
 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2378]
Underfull \hbox (badness 10000) in paragraph at lines 10784--10788
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
[2379]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2380]
Underfull \hbox (badness 10000) in paragraph at lines 10954--10956
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2381]
Underfull \hbox (badness 5036) in paragraph at lines 11010--11012
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2382]
Underfull \hbox (badness 2970) in paragraph at lines 11143--11149
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11143--11149
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2383]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
Underfull \hbox (badness 10000) in paragraph at lines 11234--11239
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11249--11251
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2384]
Underfull \vbox (badness 10000) has occurred while \output is active [2385]
Underfull \hbox (badness 2698) in paragraph at lines 11374--11380
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2386] [2387]
Underfull \hbox (badness 10000) in paragraph at lines 11467--11469
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11485--11490
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11485--11490
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11493--11498
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2388]
Underfull \hbox (badness 2057) in paragraph at lines 11565--11567
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2389]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
[2390]
Underfull \hbox (badness 5133) in paragraph at lines 11691--11695
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11691--11695
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2391]
Underfull \hbox (badness 7649) in paragraph at lines 11798--11800
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2392] [2393] [2394]
Underfull \hbox (badness 7362) in paragraph at lines 11999--12001
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2395]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2396] [2397]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2398] [2399] [2400]) (./boot-pkg.tex
Chapter 18.
[2401] [2402] [2403] [2404] [2405] [2406] [2407]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2408]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2409] [2410] [2411]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2413]
[2414]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2415]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2420] [2421] [2422] [2423] [2424]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2425] [2426] [2427]
Underfull \vbox (badness 10000) has occurred while \output is active [2428]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2429]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2430] [2431] [2432]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2433]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2434] [2435]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2436] [2437] [2438] [2439] [2440]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2441] [2442] [2443]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2444]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2445] [2446] [2447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2448] [2449] [2450] [2451] [2452] [2453] [2454]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2455] [2456]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2457] [2458] [2459]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2460]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2461] [2462]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] [2471]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2472] [2473] [2474] [2475]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2476]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2485]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2486]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2487] [2488] [2489] [2490]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2491] [2492]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2493] [2494] [2495]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2496] [2497]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2498] [2499] [2500] [2501] [2502] [2503] [2504] [2505]) (./class-pkg.tex
[2506]
Chapter 19.
[2507] [2508] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
[2518] [2519] [2520] [2521] [2522]) (./cluster-pkg.tex
Chapter 20.
[2523]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 133--142
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 133--142
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 133--142
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2524] [2525]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2526] [2527]
Underfull \vbox (badness 10000) has occurred while \output is active [2528]
[2529]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2530] [2531]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2532]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2533] [2534]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2535]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2536]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2537]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1102--1102
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2539]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1119--1119
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1157--1157
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2540]
Underfull \hbox (badness 4144) in paragraph at lines 1189--1193
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2541]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1265--1265
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1271--1271
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2542] [2543]
Underfull \hbox (badness 10000) in paragraph at lines 1410--1415
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1458--1461
[2544]
Underfull \hbox (badness 10000) in paragraph at lines 1475--1479
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1499--1499
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1509--1509
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2545]
Underfull \hbox (badness 5741) in paragraph at lines 1549--1552
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2546]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1615--1615
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2547]
Underfull \hbox (badness 1540) in paragraph at lines 1732--1740
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2548] [2549]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1823--1823
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1842--1842
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2550] [2551] [2552] [2553]
Underfull \hbox (badness 10000) in paragraph at lines 2161--2164
Underfull \hbox (badness 3179) in paragraph at lines 2175--2181
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 2333--2336
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2557]
Underfull \hbox (badness 1292) in paragraph at lines 2401--2404
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2410--2412
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2433--2436
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2558] [2559] [2560] [2561]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2649--2649
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2562] [2563] [2564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2918--2918
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2565] [2566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3021--3021
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2567] [2568] [2569]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3217--3217
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 3285--3288
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2571]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3335--3335
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572] [2573] [2574]
Underfull \hbox (badness 10000) in paragraph at lines 3521--3524
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2575]
Underfull \hbox (badness 10000) in paragraph at lines 3584--3589
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2576]
Underfull \hbox (badness 3884) in paragraph at lines 3646--3651
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3658--3661
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 3843--3846
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3874--3877
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2580]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3927--3927
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3938--3940
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2581] [2582] [2583] [2584]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4131--4131
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4133--4133
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2585] [2586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4271--4271
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4280--4280
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4282--4282
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4285--4285
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4287--4287
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4294--4294
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2587] [2588] [2589] [2590] [2591] [2592]
Underfull \hbox (badness 10000) in paragraph at lines 4652--4658
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4668--4670
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4681--4681
 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4683--4683
 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2593]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4697--4697
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2594]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2595]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2596]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2597] [2598] [2599]) (./foreign-pkg.tex [2600]
Chapter 22.
[2601]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2602] [2603]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2604]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2605] [2606] [2607]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2608]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
Underfull \hbox (badness 6001) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2609]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2610]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2611]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658
 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662
 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2612] [2613]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2614] [2615]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2616]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2621]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2622]) (./lattice-pkg.tex
Chapter 23.
[2623] [2624] [2625]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2626]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2627] [2628] [2629] [2630]
Underfull \hbox (badness 1221) in paragraph at lines 650--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2631] [2632] [2633] [2634]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2635]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2636] [2637]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2638] [2639] [2640]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2641]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2642]
Underfull \vbox (badness 10000) has occurred while \output is active [2643]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2644]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2645] [2646] [2647] [2648]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2649]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2650] [2651] [2652]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2653] [2654] [2655] [2656] [2657]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2658] [2659]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2660]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2661] [2662]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2663]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3143--3150
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2664] [2665] [2666] [2667]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2668]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2669] [2670] [2671] [2672] [2673]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2674]
Underfull \hbox (badness 2277) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2675] [2676]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2677]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4170--4174
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2678] [2679]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2680] [2681] [2682] [2683] [2684] [2685]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2686] [2687]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2688] [2689]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2690] [2691] [2692] [2693] [2694] [2695]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5486--5489
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2697]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2698]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2700] [2701]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2702] [2703]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2704] [2705]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2706] [2707]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6273--6278
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2708]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2709] [2710]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2711]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2712] [2713] [2714] [2715] [2716] [2717]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6955--6962
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2719]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
Underfull \hbox (badness 1584) in paragraph at lines 7055--7059
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2720]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2721] [2722]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2724] [2725]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
Underfull \hbox (badness 2772) in paragraph at lines 7526--7529
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2726]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2727]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2728] [2729] [2730]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2731]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2732] [2733] [2734] [2735] [2736] [2737] [2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2740] [2741]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2742]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2743]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2744]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2745] [2746]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2747] [2748]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2749]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2750] [2751] [2752] [2753] [2754] [2755] [2756]
Underfull \hbox (badness 7238) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9622--9626
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2757] [2758] [2759]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2760] [2761] [2762]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088
 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2763] [2764]) (./mgcv-pkg.tex
Chapter 24.
[2765] [2766]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2767]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152
 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2768] [2769] [2770] [2771]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2772]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408
 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2773] [2774] [2775]
Underfull \hbox (badness 2922) in paragraph at lines 607--608
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2776] [2777] [2778]
Underfull \hbox (badness 1158) in paragraph at lines 753--755
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2779]
Underfull \hbox (badness 1259) in paragraph at lines 816--817
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2780]
Underfull \vbox (badness 10000) has occurred while \output is active [2781]
[2782] [2783] [2784] [2785]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2786]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171
 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178
 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1180--1180
 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1182--1182
 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2787]
[2788]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274
 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285
 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1319--1319
 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2789]
[2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2798] [2799] [2800] [2801] [2802] [2803]
Underfull \hbox (badness 1052) in paragraph at lines 2197--2205
\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2214--2214
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Underfull \hbox (badness 1728) in paragraph at lines 2226--2229
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
Underfull \hbox (badness 1142) in paragraph at lines 2239--2243
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804]
Underfull \hbox (badness 1043) in paragraph at lines 2265--2270
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2805] [2806]
Underfull \hbox (badness 1043) in paragraph at lines 2428--2434
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2807] [2808]
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2564--2570
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2809]
Underfull \vbox (badness 10000) has occurred while \output is active [2810]
Underfull \vbox (badness 10000) has occurred while \output is active [2811]
Underfull \vbox (badness 10000) has occurred while \output is active [2812]
[2813] [2814] [2815] [2816] [2817] [2818] [2819]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3223--3223
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2820] [2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 5189) in paragraph at lines 3584--3588
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2826] [2827]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2828]
[2829] [2830]
Underfull \hbox (badness 1184) in paragraph at lines 3870--3874
[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2831] [2832] [2833] [2834] [2835] [2836] [2837]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2838] [2839] [2840]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466
 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2841]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
[2842]
Underfull \hbox (badness 1142) in paragraph at lines 4591--4595
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2843]
Underfull \hbox (badness 10000) in paragraph at lines 4660--4669
[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2844] [2845]
Underfull \hbox (badness 5970) in paragraph at lines 4777--4783
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1418) in paragraph at lines 4777--4783
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2846]
Underfull \vbox (badness 10000) has occurred while \output is active [2847]
[2848] [2849]
Underfull \hbox (badness 1577) in paragraph at lines 5057--5060
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2850] [2851] [2852] [2853] [2854] [2855] [2856]
Underfull \hbox (badness 6708) in paragraph at lines 5453--5454
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2857]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502
 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2858]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527
 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5556--5556
 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2859]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2860] [2861] [2862] [2863] [2864] [2865]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933
 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5935--5935
 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
Underfull \hbox (badness 1142) in paragraph at lines 5956--5960
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2866] [2867] [2868] [2869] [2870] [2871]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219
 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273
 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2872] [2873] [2874] [2875]
Underfull \vbox (badness 10000) has occurred while \output is active [2876]
Underfull \vbox (badness 10000) has occurred while \output is active [2877]
[2878] [2879]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6729--6729
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888]
Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2889] [2890]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359
 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2891] [2892]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422
 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7441--7441
 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2893]
[2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904]
[2905] [2906] [2907] [2908] [2909] [2910]
Underfull \vbox (badness 10000) has occurred while \output is active [2911]
[2912]
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 8661--8664
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2913]
Underfull \hbox (badness 10000) in paragraph at lines 8717--8720
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 8717--8720
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2914] [2915] [2916]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8938--8938
 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8941--8941
 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2917] [2918] [2919]
Underfull \hbox (badness 1629) in paragraph at lines 9099--9104
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2920] [2921] [2922] [2923]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310
 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2924] [2925]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474
 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2926] [2927] [2928] [2929]
Underfull \vbox (badness 10000) has occurred while \output is active [2930]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2931]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9780--9782
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
Underfull \hbox (badness 1975) in paragraph at lines 9786--9791
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2932]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2933]
Underfull \hbox (badness 10000) in paragraph at lines 9939--9942
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
Underfull \hbox (badness 2057) in paragraph at lines 9939--9942
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2934] [2935]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2936] [2937] [2938] [2939]
Underfull \hbox (badness 1946) in paragraph at lines 10247--10254
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 10247--10254
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
Underfull \hbox (badness 2846) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2940]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2941] [2942] [2943] [2944] [2945]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637
 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[2946] [2947] [2948] [2949] [2950] [2951]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985
 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 
Underfull \hbox (badness 10000) in paragraph at lines 10998--11002
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2952]
Underfull \hbox (badness 10000) in paragraph at lines 11038--11042
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2953] [2954] [2955]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2956]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 11296--11300
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2957] [2958] [2959]
Underfull \vbox (badness 10000) has occurred while \output is active [2960]
Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2961] [2962]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703
 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727
 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732
 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2965]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738
 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739
 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2966]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[2967] [2968]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2969]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[2970] [2971] [2972]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2973] [2974] [2975] [2976]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 12468--12470
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2978] [2979]
Underfull \vbox (badness 10000) has occurred while \output is active [2980]
Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12627--12630
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 12627--12630
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2981]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 12754--12760
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2983] [2984] [2985]
Underfull \vbox (badness 10000) has occurred while \output is active [2986]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2987]
Underfull \hbox (badness 10000) in paragraph at lines 13071--13079
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2988]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2989] [2990] [2991] [2992]
Underfull \hbox (badness 3396) in paragraph at lines 13358--13361
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2993]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2994] [2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13627--13630
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
[2998]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3004]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3005] [3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3007] [3008]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019]
[3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3029] [3030] [3031] [3032] [3033]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3034] [3035] [3036]) (./nlme-pkg.tex
Chapter 25.
[3037]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3039] [3040] [3041] [3042] [3043]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3044] [3045]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3054]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3055] [3056] [3057] [3058] [3059] [3060] [3061]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3062]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3063] [3064] [3065] [3066] [3067]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3069]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3070] [3071]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3072]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091]
[3092]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3093] [3094] [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103]
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114]
[3115] [3116]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3117] [3118] [3119] [3120] [3121] [3122] [3123]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3133]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3134]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3136] [3137] [3138] [3139]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3140]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3141]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3142]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3143] [3144] [3145]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3146]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3147] [3148] [3149]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3150] [3151] [3152]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3153] [3154] [3155]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3164] [3165] [3166] [3167] [3168]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3169]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3170] [3171] [3172] [3173] [3174]
[3175] [3176] [3177] [3178] [3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3182]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3183] [3184] [3185] [3186]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3187]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9750--9753
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3196] [3197] [3198]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3199]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3200] [3201] [3202]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3203] [3204]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3205]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3206] [3207] [3208] [3209]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3210] [3211] [3212] [3213] [3214] [3215]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3216] [3217] [3218] [3219] [3220] [3221]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3222] [3223] [3224] [3225]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3226] [3227] [3228] [3229] [3230]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3231] [3232]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3233]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3243] [3244] [3245] [3246] [3247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3248]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3249]
Underfull \hbox (badness 1838) in paragraph at lines 13734--13741
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13734--13741
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13798--13801
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13798--13801
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13826--13829
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13826--13829
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3252]
Underfull \hbox (badness 1472) in paragraph at lines 13931--13938
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3258] [3259] [3260] [3261]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3271] [3272] [3273]
[3274] [3275] [3276] [3277] [3278] [3279] [3280]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3281] [3282] [3283]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3284] [3285] [3286] [3287] [3288]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3289]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3290] [3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3297] [3298] [3299] [3300] [3301]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3302]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
Underfull \hbox (badness 10000) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3303] [3304] [3305] [3306]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3314]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3315]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3317]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18245--18250
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18341--18350
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 3579) in paragraph at lines 18380--18385
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3320] [3321]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18658--18667
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3333]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3334] [3335] [3336]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3338] [3339]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3340]) (./rpart-pkg.tex
Chapter 27.
[3341] [3342] [3343] [3344]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3345] [3346] [3347] [3348]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3349] [3350]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3351] [3352]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3353]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3354] [3355] [3356]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3357]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3358]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3359] [3360] [3361] [3362] [3363] [3364]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3365] [3366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3367] [3368] [3369]) (./spatial-pkg.tex [3370]
Chapter 28.
[3371] [3372] [3373] [3374] [3375] [3376]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387]
[3388] [3389]) (./survival-pkg.tex [3390]
Chapter 29.
[3391] [3392]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3393] [3394]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3395] [3396]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3397]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3398] [3399]
Underfull \vbox (badness 10000) has occurred while \output is active [3400]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3401] [3402]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3403] [3404] [3405]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3406] [3407]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3408]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                  
Underfull \vbox (badness 2698) has occurred while \output is active [3409]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271
 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3410] [3411]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3412] [3413] [3414] [3415] [3416]
Underfull \hbox (badness 1337) in paragraph at lines 1799--1803
[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854
 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3418] [3419] [3420] [3421] [3422] [3423] [3424]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351
 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3425] [3426] [3427]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3428] [3429] [3430] [3431]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3432]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894
 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
Underfull \hbox (badness 1389) in paragraph at lines 2908--2910
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3433]
Underfull \hbox (badness 1048) in paragraph at lines 2963--2965
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3434]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037
 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3435] [3436]
Underfull \vbox (badness 10000) has occurred while \output is active [3437]
Underfull \vbox (badness 10000) has occurred while \output is active [3438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3439] [3440] [3441] [3442] [3443]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560
 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3444]
Underfull \vbox (badness 10000) has occurred while \output is active [3445]
[3446] [3447] [3448] [3449] [3450]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977
 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3451] [3452]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3453]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3454]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299
 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3455]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3456] [3457]
Underfull \hbox (badness 1852) in paragraph at lines 4533--4535
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3458] [3459]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669
 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3460] [3461] [3462]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3464] [3465] [3466] [3467] [3468]
Underfull \vbox (badness 2126) has occurred while \output is active [3469]
[3470] [3471]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 1043) in paragraph at lines 5560--5563
\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3472] [3473] [3474] [3475] [3476]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3477] [3478]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3479] [3480] [3481] [3482] [3483]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3484] [3485] [3486] [3487]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3488] [3489] [3490]
Underfull \hbox (badness 1253) in paragraph at lines 6915--6918
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3491] [3492]
Underfull \hbox (badness 10000) in paragraph at lines 7041--7050
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
Underfull \hbox (badness 3758) in paragraph at lines 7041--7050
\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3493]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137
 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3494]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
Underfull \hbox (badness 1038) in paragraph at lines 7197--7203
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3495]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3496]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3497] [3498] [3499]
Underfull \hbox (badness 10000) in paragraph at lines 7560--7565
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
[3500]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3501] [3502]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3503] [3504] [3505]
Underfull \hbox (badness 3058) in paragraph at lines 7969--7974
[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
Underfull \hbox (badness 7759) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
Underfull \hbox (badness 2913) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
Underfull \hbox (badness 4353) in paragraph at lines 7969--7974
\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
[3506]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3507] [3508] [3509] [3510]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3511]
Underfull \hbox (badness 1354) in paragraph at lines 8422--8426
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3512] [3513]
Underfull \hbox (badness 2035) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 8597--8604
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 8597--8604
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3514]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3515] [3516] [3517]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3518] [3519]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8965--8965
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3520] [3521] [3522] [3523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267
 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9268--9268
 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3524]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274
 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9276--9276
 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3525] [3526] [3527] [3528] [3529] [3530] [3531]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727
 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3532] [3533] [3534]) (./fullrefman.ind [3535] [3536] [3537] [3538] [3539]
[3540] [3541] [3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550]
[3551] [3552] [3553] [3554] [3555]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2205--2207
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2207--2209
[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2209--2211
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2211--2213
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2213--2215
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2215--2217
[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2217--2219
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2219--2221
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2221--2223
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2223--2225
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2225--2227
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2227--2229
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (43.3567pt too wide) in paragraph at lines 2229--2231
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2231--2233
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3556] [3557] [3558] [3559] [3560]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2771--2773
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2773--2775
[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2775--2777
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2777--2779
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2779--2781
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2781--2783
[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2783--2785
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2785--2787
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2787--2789
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2789--2791
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2791--2793
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
[3561]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2793--2795
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (43.3567pt too wide) in paragraph at lines 2795--2797
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2797--2799
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3562]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2934--2936
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3563] [3564] [3565] [3566] [3567] [3568] [3569] [3570]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3939--3941
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3941--3943
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3943--3945
[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3947--3949
[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 3949--3951
[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3951--3953
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3953--3955
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3955--3957
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3957--3959
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 3959--3961
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 3961--3963
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 3963--3965
[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 3965--3967
[]\T1/pcr/m/n/10 [,Matrix,missing,missing,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3967--3969
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,index,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3969--3971
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,missing,logical-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 3971--3973
[]\T1/pcr/m/n/10 [,TsparseMatrix,missing,index,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 3975--3977
[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 3977--3979
[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 3979--3981
[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3981--3983
[]\T1/pcr/m/n/10 [,denseMatrix,index,missing,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 3983--3985
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3985--3987
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3987--3989
[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3989--3991
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 3991--3993
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 3993--3995
[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 3995--3997
[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 3997--3999
[]\T1/pcr/m/n/10 [,sparseMatrix,index,index,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3999--4001
[]\T1/pcr/m/n/10 [,sparseMatrix,index,missing,logical-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4001--4003
[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4003--4005
[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4005--4007
[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4007--4009
[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method 
[3571]
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4083--4085
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4085--4087
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4087--4089
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4089--4091
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4091--4093
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (140.8567pt too wide) in paragraph at lines 4093--4095
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4095--4097
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,lsparseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4097--4099
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4099--4101
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4101--4103
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,sparseVector-method 
Overfull \hbox (140.8567pt too wide) in paragraph at lines 4103--4105
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ndenseMatrix,missing,replValue-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4105--4107
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,nsparseMatrix,missing,replValue-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4109--4111
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4111--4113
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4113--4115
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4115--4117
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,matrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4117--4119
[]\T1/pcr/m/n/10 [<-,Matrix,ldenseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4119--4121
[]\T1/pcr/m/n/10 [<-,Matrix,lsparseMatrix,missing,replValue-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4121--4123
[]\T1/pcr/m/n/10 [<-,Matrix,matrix,missing,replValue-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4123--4125
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4125--4127
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,matrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4127--4129
[]\T1/pcr/m/n/10 [<-,Matrix,ndenseMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4129--4131
[]\T1/pcr/m/n/10 [<-,Matrix,nsparseMatrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4131--4133
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4133--4135
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4135--4137
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4137--4139
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4139--4141
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4141--4143
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4143--4145
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,sparseVector-method 
[3572]
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4145--4147
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,Matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4147--4149
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4149--4151
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,sparseVector-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4151--4153
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4153--4155
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4155--4157
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,lMatrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4157--4159
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,matrix,missing,replValue-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4159--4161
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,replValue-method 
Overfull \hbox (116.8567pt too wide) in paragraph at lines 4161--4163
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4163--4165
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,nMatrix,missing,replValue-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 4165--4167
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,index,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4167--4169
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,missing,replValue-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 4169--4171
[]\T1/pcr/m/n/10 [<-,denseMatrix,matrix,missing,replValue-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 4171--4173
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,index,replValue-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4173--4175
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,missing,ANY-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 4175--4177
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,replValue-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4177--4179
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseMatrix-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4179--4181
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseVector-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4181--4183
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,replValue-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4183--4185
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseMatrix-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4185--4187
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseVector-method 
Overfull \hbox (110.8567pt too wide) in paragraph at lines 4187--4189
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,matrix,missing,replValue-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4189--4191
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,replValue-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4191--4193
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseMatrix-method 
Overfull \hbox (122.8567pt too wide) in paragraph at lines 4193--4195
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseVector-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 4195--4197
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4197--4199
[]\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4199--4201
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4201--4203
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 4203--4205
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4205--4207
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method 
Overfull \hbox (98.8567pt too wide) in paragraph at lines 4207--4209
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 4209--4211
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method 
Overfull \hbox (104.8567pt too wide) in paragraph at lines 4211--4213
[]\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValueSp-method 
Overfull \hbox (146.8567pt too wide) in paragraph at lines 4213--4215
[]\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValueSp-method 
[3573]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4292--4294
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4294--4296
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4296--4298
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4300--4302
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4318--4320
[]\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method 
Underfull \vbox (badness 1824) has occurred while \output is active
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4326--4328
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4328--4330
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4330--4332
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4332--4334
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4334--4336
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dtrMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4336--4338
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4340--4342
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4342--4344
[]\T1/pcr/m/n/10 %*%,denseMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4346--4348
[]\T1/pcr/m/n/10 %*%,dgeMatrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4348--4350
[]\T1/pcr/m/n/10 %*%,dgeMatrix,dsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4356--4358
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4358--4360
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4360--4362
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,dgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4362--4364
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4364--4366
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4366--4368
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4368--4370
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4370--4372
[]\T1/pcr/m/n/10 %*%,dspMatrix,ddenseMatrix-method 
[3574]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4374--4376
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4376--4378
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4378--4380
[]\T1/pcr/m/n/10 %*%,dsyMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4384--4386
[]\T1/pcr/m/n/10 %*%,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4388--4390
[]\T1/pcr/m/n/10 %*%,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4408--4410
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4410--4412
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4412--4414
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4416--4418
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 4420--4422
[]\T1/pcr/m/n/10 %*%,lgeMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4422--4424
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4424--4426
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4436--4438
[]\T1/pcr/m/n/10 %*%,matrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4460--4462
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4462--4464
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4466--4468
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4468--4470
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 4472--4474
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4474--4476
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4476--4478
[]\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method 
[3575]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4490--4492
[]\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4498--4500
[]\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4506--4508
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4508--4510
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4510--4512
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4514--4516
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4516--4518
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4518--4520
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4524--4526
[]\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4526--4528
[]\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4528--4530
[]\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4532--4534
[]\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4534--4536
[]\T1/pcr/m/n/10 %%,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4536--4538
[]\T1/pcr/m/n/10 %%,ldiMatrix,ndenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4546--4548
[]\T1/pcr/m/n/10 %&%,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4552--4554
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4554--4556
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4556--4558
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,geMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4558--4560
[]\T1/pcr/m/n/10 %&%,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4560--4562
[]\T1/pcr/m/n/10 %&%,geMatrix,diagonalMatrix-method 
Underfull \vbox (badness 4328) has occurred while \output is active [3576]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4572--4574
[]\T1/pcr/m/n/10 %&%,nCsparseMatrix,nCsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4574--4576
[]\T1/pcr/m/n/10 %&%,nCsparseMatrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4580--4582
[]\T1/pcr/m/n/10 %&%,nMatrix,nsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 4582--4584
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nCsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4584--4586
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4586--4588
[]\T1/pcr/m/n/10 %&%,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 4590--4592
[]\T1/pcr/m/n/10 %&%,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4596--4598
[]\T1/pcr/m/n/10 %&%,sparseVector,sparseVector-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3577]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 4771--4773
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3578]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4915--4917
[]\T1/pcr/m/n/10 all.equal,abIndex,abIndex-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4917--4919
[]\T1/pcr/m/n/10 all.equal,abIndex,numLike-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4921--4923
[]\T1/pcr/m/n/10 all.equal,ANY,sparseMatrix-method 
Underfull \vbox (badness 1226) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4923--4925
[]\T1/pcr/m/n/10 all.equal,ANY,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4929--4931
[]\T1/pcr/m/n/10 all.equal,numLike,abIndex-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4931--4933
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4933--4935
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4935--4937
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4937--4939
[]\T1/pcr/m/n/10 all.equal,sparseVector,ANY-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4939--4941
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 4941--4943
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseVector-method 
[3579]
Underfull \vbox (badness 1348) has occurred while \output is active
Overfull \hbox (50.8567pt too wide) in paragraph at lines 5200--5202
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5202--5204
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5204--5206
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5206--5208
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method 
[3580]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5208--5210
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5210--5212
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5216--5218
[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5222--5224
[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 5228--5230
[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5240--5242
[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5242--5244
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5244--5246
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 5246--5248
[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5248--5250
[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5254--5256
[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5256--5258
[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5258--5260
[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5264--5266
[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5276--5278
[]\T1/pcr/m/n/10 Arith,logical,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5284--5286
[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5286--5288
[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5290--5292
[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 5292--5294
[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5298--5300
[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method 
Underfull \vbox (badness 4328) has occurred while \output is active [3581]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5300--5302
[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 5302--5304
[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5314--5316
[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5324--5326
[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 5326--5328
[]\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 5328--5330
[]\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 5330--5332
[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1824) has occurred while \output is active [3582]
Underfull \vbox (badness 1348) has occurred while \output is active [3583]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 5813--5815
[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file 
[3584]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 5975--5977
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3585] [3586] [3587]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6599--6601
[]\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6601--6603
[]\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6603--6605
[]\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6605--6607
[]\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 6609--6611
[]\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 6611--6613
[]\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6613--6615
[]\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 6615--6617
[]\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6617--6619
[]\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 6619--6621
[]\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6625--6627
[]\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 6629--6631
[]\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6639--6641
[]\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3588]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6643--6645
[]\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6645--6647
[]\T1/pcr/m/n/10 cbind2,numeric,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 6647--6649
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6649--6651
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6651--6653
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6653--6655
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 6655--6657
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method 
[3589]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 6890--6892
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Underfull \vbox (badness 1019) has occurred while \output is active [3590]
[3591] [3592]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7377--7379
[]\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7379--7381
[]\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7381--7383
[]\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7387--7389
[]\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7389--7391
[]\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7393--7395
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7395--7397
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7397--7399
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lsparseMatrix-method 
Underfull \vbox (badness 2564) has occurred while \output is active
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7399--7401
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.coo-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7401--7403
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csc-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7403--7405
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csr-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7405--7407
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7407--7409
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7409--7411
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 7411--7413
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,symmetricMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7413--7415
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7415--7417
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7417--7419
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7419--7421
[]\T1/pcr/m/n/10 coerce,ddiMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7421--7423
[]\T1/pcr/m/n/10 coerce,ddiMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7423--7425
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dgeMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7425--7427
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7429--7431
[]\T1/pcr/m/n/10 coerce,ddiMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7431--7433
[]\T1/pcr/m/n/10 coerce,ddiMatrix,triangularMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7433--7435
[]\T1/pcr/m/n/10 coerce,ddiMatrix,TsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7435--7437
[]\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7437--7439
[]\T1/pcr/m/n/10 coerce,denseMatrix,generalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7439--7441
[]\T1/pcr/m/n/10 coerce,denseMatrix,RsparseMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3593]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7441--7443
[]\T1/pcr/m/n/10 coerce,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7443--7445
[]\T1/pcr/m/n/10 coerce,denseMatrix,symmetricMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7445--7447
[]\T1/pcr/m/n/10 coerce,denseMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7447--7449
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7449--7451
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7451--7453
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7453--7455
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7455--7457
[]\T1/pcr/m/n/10 coerce,dgCMatrix,lgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7459--7461
[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7461--7463
[]\T1/pcr/m/n/10 coerce,dgCMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7465--7467
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7467--7469
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7469--7471
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7471--7473
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7473--7475
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7475--7477
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7477--7479
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7479--7481
[]\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7483--7485
[]\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7485--7487
[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7487--7489
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7489--7491
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method 
Underfull \vbox (badness 2903) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7491--7493
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7493--7495
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7495--7497
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtTMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7497--7499
[]\T1/pcr/m/n/10 coerce,dgTMatrix,graphNEL-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7501--7503
[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7503--7505
[]\T1/pcr/m/n/10 coerce,dgTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7505--7507
[]\T1/pcr/m/n/10 coerce,dgTMatrix,triangularMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7507--7509
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,denseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 7509--7511
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,generalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7511--7513
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7513--7515
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 7515--7517
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7517--7519
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7523--7525
[]\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7525--7527
[]\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7531--7533
[]\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7533--7535
[]\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3594]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7539--7541
[]\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7541--7543
[]\T1/pcr/m/n/10 coerce,dsCMatrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7543--7545
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7545--7547
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7547--7549
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7549--7551
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsRMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7551--7553
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7553--7555
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsyMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7555--7557
[]\T1/pcr/m/n/10 coerce,dsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7557--7559
[]\T1/pcr/m/n/10 coerce,dsCMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7561--7563
[]\T1/pcr/m/n/10 coerce,dsCMatrix,nsCMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7565--7567
[]\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7567--7569
[]\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7569--7571
[]\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7571--7573
[]\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7573--7575
[]\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7575--7577
[]\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7579--7581
[]\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7581--7583
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7583--7585
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7585--7587
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7587--7589
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7589--7591
[]\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7593--7595
[]\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7595--7597
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7597--7599
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7599--7601
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7601--7603
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7603--7605
[]\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7607--7609
[]\T1/pcr/m/n/10 coerce,dtCMatrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7609--7611
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7611--7613
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7613--7615
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7615--7617
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7617--7619
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7619--7621
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7621--7623
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7623--7625
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ltCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7627--7629
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ntCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7629--7631
[]\T1/pcr/m/n/10 coerce,dtCMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7631--7633
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7633--7635
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7635--7637
[]\T1/pcr/m/n/10 coerce,dtpMatrix,ltpMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7639--7641
[]\T1/pcr/m/n/10 coerce,dtrMatrix,CsparseMatrix-method 
[3595]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7641--7643
[]\T1/pcr/m/n/10 coerce,dtrMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7643--7645
[]\T1/pcr/m/n/10 coerce,dtrMatrix,ltrMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7647--7649
[]\T1/pcr/m/n/10 coerce,dtrMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7649--7651
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7651--7653
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7653--7655
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7655--7657
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7657--7659
[]\T1/pcr/m/n/10 coerce,dtTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7663--7665
[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7665--7667
[]\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7669--7671
[]\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7671--7673
[]\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7673--7675
[]\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7675--7677
[]\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7677--7679
[]\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7679--7681
[]\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7683--7685
[]\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7687--7689
[]\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7691--7693
[]\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7693--7695
[]\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7697--7699
[]\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7699--7701
[]\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7705--7707
[]\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7707--7709
[]\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7709--7711
[]\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7711--7713
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7713--7715
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7715--7717
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7717--7719
[]\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7719--7721
[]\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7721--7723
[]\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7723--7725
[]\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7725--7727
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7727--7729
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7729--7731
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7731--7733
[]\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method 
[3596]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7735--7737
[]\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7737--7739
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7739--7741
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7741--7743
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7743--7745
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7745--7747
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7747--7749
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7751--7753
[]\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7753--7755
[]\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7755--7757
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7757--7759
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7759--7761
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7761--7763
[]\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 7765--7767
[]\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7767--7769
[]\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7779--7781
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7781--7783
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7783--7785
[]\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7785--7787
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7787--7789
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7789--7791
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7793--7795
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7795--7797
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7797--7799
[]\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7799--7801
[]\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7801--7803
[]\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7803--7805
[]\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7805--7807
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7807--7809
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7809--7811
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7811--7813
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method 
Underfull \vbox (badness 6876) has occurred while \output is active [3597]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7815--7817
[]\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7817--7819
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7819--7821
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7823--7825
[]\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7825--7827
[]\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7827--7829
[]\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7831--7833
[]\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7833--7835
[]\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7835--7837
[]\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7837--7839
[]\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7839--7841
[]\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7841--7843
[]\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7843--7845
[]\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7845--7847
[]\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7847--7849
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7849--7851
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7851--7853
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method 
Underfull \vbox (badness 5847) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7853--7855
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7863--7865
[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7865--7867
[]\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 7867--7869
[]\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7877--7879
[]\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7879--7881
[]\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3598]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7909--7911
[]\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7939--7941
[]\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7965--7967
[]\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 7967--7969
[]\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 7969--7971
[]\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 7971--7973
[]\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7973--7975
[]\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7975--7977
[]\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7979--7981
[]\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7981--7983
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7983--7985
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7987--7989
[]\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7989--7991
[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3599]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7991--7993
[]\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7995--7997
[]\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7997--7999
[]\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7999--8001
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8001--8003
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 8005--8007
[]\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 8007--8009
[]\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8009--8011
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8011--8013
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8013--8015
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8015--8017
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8017--8019
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8019--8021
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8021--8023
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8025--8027
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8027--8029
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8031--8033
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8035--8037
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8037--8039
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8039--8041
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8041--8043
[]\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8043--8045
[]\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8047--8049
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8049--8051
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8051--8053
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8053--8055
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8055--8057
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8057--8059
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8059--8061
[]\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8061--8063
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8065--8067
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8067--8069
[]\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8069--8071
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8071--8073
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method 
[3600]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8077--8079
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8079--8081
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8081--8083
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8083--8085
[]\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8085--8087
[]\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8099--8101
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8101--8103
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8103--8105
[]\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8107--8109
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8109--8111
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8113--8115
[]\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8115--8117
[]\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8117--8119
[]\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8119--8121
[]\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8121--8123
[]\T1/pcr/m/n/10 coerce,nsparseVector,isparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8123--8125
[]\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8125--8127
[]\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8127--8129
[]\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8129--8131
[]\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8131--8133
[]\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8133--8135
[]\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8135--8137
[]\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8139--8141
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8141--8143
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8143--8145
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8145--8147
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8147--8149
[]\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8149--8151
[]\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8151--8153
[]\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8153--8155
[]\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method 
Underfull \vbox (badness 5022) has occurred while \output is active [3601]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8157--8159
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8159--8161
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8163--8165
[]\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8165--8167
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8169--8171
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8171--8173
[]\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8173--8175
[]\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8175--8177
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8177--8179
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8179--8181
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ntrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8181--8183
[]\T1/pcr/m/n/10 coerce,ntrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8183--8185
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ltrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8185--8187
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ngeMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8187--8189
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ntpMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8189--8191
[]\T1/pcr/m/n/10 coerce,ntTMatrix,dtTMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8191--8193
[]\T1/pcr/m/n/10 coerce,ntTMatrix,generalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8195--8197
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8197--8199
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8199--8201
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8201--8203
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8205--8207
[]\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8213--8215
[]\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8219--8221
[]\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8223--8225
[]\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8227--8229
[]\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8239--8241
[]\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8241--8243
[]\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8243--8245
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method 
[3602]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8245--8247
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 8247--8249
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8249--8251
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8251--8253
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8253--8255
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8255--8257
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8257--8259
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8259--8261
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8261--8263
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8265--8267
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8271--8273
[]\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 8273--8275
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8275--8277
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 8277--8279
[]\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8281--8283
[]\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8283--8285
[]\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8285--8287
[]\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 8287--8289
[]\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8289--8291
[]\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8291--8293
[]\T1/pcr/m/n/10 coerce,sparseVector,integer-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8293--8295
[]\T1/pcr/m/n/10 coerce,sparseVector,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8295--8297
[]\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8297--8299
[]\T1/pcr/m/n/10 coerce,sparseVector,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 8299--8301
[]\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8301--8303
[]\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8303--8305
[]\T1/pcr/m/n/10 coerce,sparseVector,vector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 8305--8307
[]\T1/pcr/m/n/10 coerce,table,sparseMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 8307--8309
[]\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8309--8311
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 8311--8313
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8313--8315
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8315--8317
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8317--8319
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 8319--8321
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8321--8323
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 8323--8325
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8325--8327
[]\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8327--8329
[]\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8329--8331
[]\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8331--8333
[]\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 8333--8335
[]\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method 
[3603]
Underfull \vbox (badness 1117) has occurred while \output is active
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8471--8473
[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8477--8479
[]\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 8489--8491
[]\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 8491--8493
[]\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method 
[3604]
Overfull \hbox (86.8567pt too wide) in paragraph at lines 8505--8507
[]\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method 
[3605] [3606]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9034--9036
[]\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9036--9038
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9038--9040
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 9040--9042
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9042--9044
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9044--9046
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9046--9048
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9048--9050
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9050--9052
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9052--9054
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9054--9056
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dsparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9056--9058
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9058--9060
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9060--9062
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9062--9064
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9064--9066
[]\T1/pcr/m/n/10 crossprod,dgCMatrix,dgeMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9066--9068
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dgeMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9068--9070
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9070--9072
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9072--9074
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9074--9076
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,numLike-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 9076--9078
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,CsparseMatrix-method 
Underfull \vbox (badness 2564) has occurred while \output is active [3607]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9078--9080
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,dgeMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 9080--9082
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9082--9084
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,lgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9084--9086
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9086--9088
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,missing-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9088--9090
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9090--9092
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,ddenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9092--9094
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,dgeMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9094--9096
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9096--9098
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9098--9100
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9100--9102
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,dtrMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9102--9104
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9104--9106
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9106--9108
[]\T1/pcr/m/n/10 crossprod,indMatrix,indMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9108--9110
[]\T1/pcr/m/n/10 crossprod,indMatrix,Matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9110--9112
[]\T1/pcr/m/n/10 crossprod,indMatrix,matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9112--9114
[]\T1/pcr/m/n/10 crossprod,indMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9114--9116
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9116--9118
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9118--9120
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9120--9122
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9122--9124
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9124--9126
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9126--9128
[]\T1/pcr/m/n/10 crossprod,lgCMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9128--9130
[]\T1/pcr/m/n/10 crossprod,lgTMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9130--9132
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9132--9134
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9134--9136
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9140--9142
[]\T1/pcr/m/n/10 crossprod,matrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9142--9144
[]\T1/pcr/m/n/10 crossprod,matrix,dgeMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9144--9146
[]\T1/pcr/m/n/10 crossprod,matrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9146--9148
[]\T1/pcr/m/n/10 crossprod,matrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9158--9160
[]\T1/pcr/m/n/10 crossprod,Matrix,TsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9160--9162
[]\T1/pcr/m/n/10 crossprod,mMatrix,sparseVector-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9162--9164
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9164--9166
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9166--9168
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,matrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9168--9170
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9170--9172
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9172--9174
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,nsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9174--9176
[]\T1/pcr/m/n/10 crossprod,ngCMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9176--9178
[]\T1/pcr/m/n/10 crossprod,ngTMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9178--9180
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 9180--9182
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,ndenseMatrix-method 
[3608]
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9182--9184
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,nsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9186--9188
[]\T1/pcr/m/n/10 crossprod,numLike,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9188--9190
[]\T1/pcr/m/n/10 crossprod,numLike,dgeMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9192--9194
[]\T1/pcr/m/n/10 crossprod,numLike,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 9198--9200
[]\T1/pcr/m/n/10 crossprod,pMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 9200--9202
[]\T1/pcr/m/n/10 crossprod,pMatrix,pMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9202--9204
[]\T1/pcr/m/n/10 crossprod,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9204--9206
[]\T1/pcr/m/n/10 crossprod,sparseVector,missing-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9206--9208
[]\T1/pcr/m/n/10 crossprod,sparseVector,mMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9208--9210
[]\T1/pcr/m/n/10 crossprod,sparseVector,numLike-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 9210--9212
[]\T1/pcr/m/n/10 crossprod,sparseVector,sparseVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9212--9214
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9214--9216
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9216--9218
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9218--9220
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 9220--9222
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 9222--9224
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 9224--9226
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9258--9260
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9319--9321
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 9324--9326
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3609] [3610]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 9633--9635
[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9658--9660
[]\T1/pcr/m/n/10 determinant,CHMfactor,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9660--9662
[]\T1/pcr/m/n/10 determinant,CHMfactor,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9662--9664
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9664--9666
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9666--9668
[]\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9668--9670
[]\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9670--9672
[]\T1/pcr/m/n/10 determinant,dgeMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9672--9674
[]\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9674--9676
[]\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9676--9678
[]\T1/pcr/m/n/10 determinant,dpoMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9678--9680
[]\T1/pcr/m/n/10 determinant,dppMatrix,logical-method 
Underfull \vbox (badness 1226) has occurred while \output is active
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9680--9682
[]\T1/pcr/m/n/10 determinant,dppMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9682--9684
[]\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9684--9686
[]\T1/pcr/m/n/10 determinant,dsCMatrix,missing-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 9686--9688
[]\T1/pcr/m/n/10 determinant,dsparseMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9688--9690
[]\T1/pcr/m/n/10 determinant,dtCMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9690--9692
[]\T1/pcr/m/n/10 determinant,dtpMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9692--9694
[]\T1/pcr/m/n/10 determinant,dtpMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9694--9696
[]\T1/pcr/m/n/10 determinant,dtrMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9696--9698
[]\T1/pcr/m/n/10 determinant,dtrMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 9698--9700
[]\T1/pcr/m/n/10 determinant,indMatrix,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9700--9702
[]\T1/pcr/m/n/10 determinant,Matrix,logical-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 9702--9704
[]\T1/pcr/m/n/10 determinant,Matrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 9704--9706
[]\T1/pcr/m/n/10 determinant,pMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9706--9708
[]\T1/pcr/m/n/10 determinant,sparseMatrix,logical-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9708--9710
[]\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method 
[3611] [3612]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 10031--10033
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10101--10103
[]\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10103--10105
[]\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method 
[3613]
Underfull \vbox (badness 1117) has occurred while \output is active [3614]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 10424--10426
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3615]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10730--10732
[]\T1/pcr/m/n/10 expand,MatrixFactorization-method 
Overfull \hbox (10.01662pt too wide) in paragraph at lines 10730--10732
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
[3616]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 10927--10929
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3617] [3618]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11250--11252
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11252--11254
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11254--11256
[]\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 11256--11258
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11258--11260
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11260--11262
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11262--11264
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11264--11266
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11266--11268
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11268--11270
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11270--11272
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11272--11274
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11274--11276
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11276--11278
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11278--11280
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11280--11282
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11282--11284
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11284--11286
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11286--11288
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11288--11290
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11290--11292
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11292--11294
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11294--11296
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11296--11298
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11298--11300
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11300--11302
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11302--11304
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11304--11306
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11306--11308
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 11308--11310
[]\T1/pcr/m/n/10 forceSymmetric,matrix,ANY-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 11310--11312
[]\T1/pcr/m/n/10 forceSymmetric,Matrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11312--11314
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11314--11316
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11316--11318
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11318--11320
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11320--11322
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11322--11324
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,missing-method 
[3619]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11324--11326
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11326--11328
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,missing-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 11328--11330
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,character-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 11330--11332
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 11332--11334
[]\T1/pcr/m/n/10 forceSymmetric,sparseMatrix,ANY-method 
[3620] [3621] [3622] [3623]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 12248--12250
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3624]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 12568--12570
[]\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class 
[3625] [3626]
Underfull \vbox (badness 5022) has occurred while \output is active [3627]
[3628]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13320--13322
[]\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13322--13324
[]\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13330--13332
[]\T1/pcr/m/n/10 is.infinite,nsparseVector-method 
[3629]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13492--13494
[]\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13498--13500
[]\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13500--13502
[]\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13566--13568
[]\T1/pcr/m/n/10 isSymmetric,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13572--13574
[]\T1/pcr/m/n/10 isSymmetric,symmetricMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13574--13576
[]\T1/pcr/m/n/10 isSymmetric,triangularMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 13580--13582
[]\T1/pcr/m/n/10 isTriangular,BunchKaufman-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13584--13586
[]\T1/pcr/m/n/10 isTriangular,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 13588--13590
[]\T1/pcr/m/n/10 isTriangular,diagonalMatrix-method 
[3630]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13622--13624
[]\T1/pcr/m/n/10 isTriangular,pBunchKaufman-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13626--13628
[]\T1/pcr/m/n/10 isTriangular,triangularMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13628--13630
[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13725--13727
[]\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13729--13731
[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13731--13733
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13733--13735
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 13735--13737
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 13737--13739
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 13739--13741
[]\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13741--13743
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13743--13745
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method 
[3631]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 13745--13747
[]\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 13749--13751
[]\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 13751--13753
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 13753--13755
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 13755--13757
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 13757--13759
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method 
[3632] [3633] [3634]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14533--14535
[]\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14539--14541
[]\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 14541--14543
[]\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14543--14545
[]\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14545--14547
[]\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14547--14549
[]\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14553--14555
[]\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14563--14565
[]\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 14565--14567
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14567--14569
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14569--14571
[]\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14571--14573
[]\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14579--14581
[]\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active [3635]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14589--14591
[]\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 14591--14593
[]\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14599--14601
[]\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14601--14603
[]\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14603--14605
[]\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 14605--14607
[]\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 14607--14609
[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method 
Underfull \vbox (badness 2035) has occurred while \output is active [3636]
[3637] [3638] [3639]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 15596--15598
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3640] [3641] [3642]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16152--16154
[]\T1/pcr/m/n/10 nonstandardGenericWithTrace-class 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16171--16173
[]\T1/pcr/m/n/10 norm,ddenseMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 16173--16175
[]\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16179--16181
[]\T1/pcr/m/n/10 norm,diagonalMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16197--16199
[]\T1/pcr/m/n/10 norm,ldenseMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16203--16205
[]\T1/pcr/m/n/10 norm,ndenseMatrix,character-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 16205--16207
[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method 
Underfull \vbox (badness 1824) has occurred while \output is active [3643]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16457--16459
[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 16463--16465
[]\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1642) has occurred while \output is active [3644]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16475--16477
[]\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 16477--16479
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 16479--16481
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16481--16483
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 16483--16485
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16503--16505
[]\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16505--16507
[]\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16521--16523
[]\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16541--16543
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16543--16545
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method 
[3645]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16563--16565
[]\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16571--16573
[]\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16575--16577
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16577--16579
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16579--16581
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16599--16601
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16601--16603
[]\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 16603--16605
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16605--16607
[]\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16609--16611
[]\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16613--16615
[]\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 16617--16619
[]\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method 
[3646]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 16820--16822
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (77.3567pt too wide) in paragraph at lines 16846--16848
[]\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 
[3647]
Underfull \vbox (badness 1348) has occurred while \output is active [3648]
Underfull \vbox (badness 1117) has occurred while \output is active
Underfull \vbox (badness 1642) has occurred while \output is active [3649]
[3650] [3651] [3652]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18118--18120
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18121--18123
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18123--18125
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18125--18127
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18127--18129
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18129--18131
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (52.01662pt too wide) in paragraph at lines 18131--18133
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18133--18135
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 18135--18137
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18137--18139
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (52.01662pt too wide) in paragraph at lines 18141--18143
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18143--18145
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18145--18147
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18147--18149
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18149--18151
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18151--18153
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3653] [3654]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18501--18503
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3655]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 18573--18575
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
Underfull \vbox (badness 1642) has occurred while \output is active [3656]
[3657]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19037--19039
[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19046--19048
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19048--19050
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19050--19052
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19052--19054
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19064--19066
[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 
[3658]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19074--19076
[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 19089--19091
[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19095--19097
[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 19211--19213
[]\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[3659]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19418--19420
[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19420--19422
[]\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19422--19424
[]\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19424--19426
[]\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method 
[3660]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 19428--19430
[]\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19430--19432
[]\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19432--19434
[]\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19434--19436
[]\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 19436--19438
[]\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19438--19440
[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 19440--19442
[]\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19446--19448
[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19450--19452
[]\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19460--19462
[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19464--19466
[]\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19466--19468
[]\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 19468--19470
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method 
Overfull \hbox (56.8567pt too wide) in paragraph at lines 19470--19472
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19472--19474
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method 
Underfull \vbox (badness 3769) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19474--19476
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 19476--19478
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19505--19507
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 19507--19509
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 19509--19511
[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19511--19513
[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19515--19517
[]\T1/pcr/m/n/10 rcond,dpoMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19519--19521
[]\T1/pcr/m/n/10 rcond,dppMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19523--19525
[]\T1/pcr/m/n/10 rcond,dspMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19527--19529
[]\T1/pcr/m/n/10 rcond,dsyMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19531--19533
[]\T1/pcr/m/n/10 rcond,dtpMatrix,character-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 19535--19537
[]\T1/pcr/m/n/10 rcond,dtrMatrix,character-method 
Underfull \vbox (badness 1348) has occurred while \output is active [3661]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19539--19541
[]\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19543--19545
[]\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 19545--19547
[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method 
[3662] [3663] [3664] [3665]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20499--20501
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20501--20503
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20505--20507
[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20507--20509
[]\T1/pcr/m/n/10 Schur,generalMatrix,missing-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20513--20515
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20515--20517
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method 
[3666]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20517--20519
[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20519--20521
[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method 
[3667]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 20904--20906
[]\T1/pcr/m/n/10 show,genericFunctionWithTrace-method 
Overfull \hbox (10.01662pt too wide) in paragraph at lines 20908--20910
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 20912--20914
[]\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 20916--20918
[]\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method 
Underfull \vbox (badness 2564) has occurred while \output is active [3668]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 20926--20928
[]\T1/pcr/m/n/10 show,refClassRepresentation-method 
[3669]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21166--21168
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21168--21170
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21171--21173
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (5.3567pt too wide) in paragraph at lines 21177--21178
[]\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21186--21188
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (5.3567pt too wide) in paragraph at lines 21191--21192
[]\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21192--21194
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (23.3567pt too wide) in paragraph at lines 21195--21199
[]\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21200--21202
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
Overfull \hbox (46.01662pt too wide) in paragraph at lines 21248--21250
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3670]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21281--21283
[]\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 21283--21285
[]\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21285--21287
[]\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21295--21297
[]\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21297--21299
[]\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 21299--21301
[]\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 21301--21303
[]\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21305--21307
[]\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21307--21309
[]\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21313--21315
[]\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21319--21321
[]\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method 
Underfull \vbox (badness 2035) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21321--21323
[]\T1/pcr/m/n/10 solve,diagonalMatrix,Matrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21323--21325
[]\T1/pcr/m/n/10 solve,diagonalMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21325--21327
[]\T1/pcr/m/n/10 solve,diagonalMatrix,missing-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21327--21329
[]\T1/pcr/m/n/10 solve,dpoMatrix,dgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21333--21335
[]\T1/pcr/m/n/10 solve,dppMatrix,dgeMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21341--21343
[]\T1/pcr/m/n/10 solve,dsCMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21343--21345
[]\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21345--21347
[]\T1/pcr/m/n/10 solve,dsCMatrix,dsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21353--21355
[]\T1/pcr/m/n/10 solve,dspMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21359--21361
[]\T1/pcr/m/n/10 solve,dsyMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21361--21363
[]\T1/pcr/m/n/10 solve,dsyMatrix,denseMatrix-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21367--21369
[]\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21369--21371
[]\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method 
[3671]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21377--21379
[]\T1/pcr/m/n/10 solve,dtpMatrix,ddenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 21383--21385
[]\T1/pcr/m/n/10 solve,dtrMatrix,ddenseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21395--21397
[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 21407--21409
[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method 
Overfull \hbox (26.8567pt too wide) in paragraph at lines 21409--21411
[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 21411--21413
[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 21413--21415
[]\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 21425--21427
[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method 
[3672]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 21573--21575
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3673] [3674]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22011--22013
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22013--22015
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22015--22017
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings 
[3675] [3676] [3677] [3678]
Underfull \vbox (badness 5022) has occurred while \output is active [3679]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22879--22881
[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22881--22883
[]\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 22883--22885
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 22885--22887
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 22887--22889
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22889--22891
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22891--22893
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22893--22895
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method 
Overfull \hbox (74.8567pt too wide) in paragraph at lines 22895--22897
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22897--22899
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ddenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22899--22901
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22901--22903
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dtrMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22903--22905
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ldenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22905--22907
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,lsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22907--22909
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22909--22911
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22911--22913
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ndenseMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22913--22915
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22915--22917
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 22917--22919
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method 
Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22919--22921
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22921--22923
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22923--22925
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method 
Overfull \hbox (86.8567pt too wide) in paragraph at lines 22925--22927
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method 
Overfull \hbox (92.8567pt too wide) in paragraph at lines 22927--22929
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22929--22931
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,matrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22931--22933
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 22933--22935
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,sparseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22935--22937
[]\T1/pcr/m/n/10 tcrossprod,dtrMatrix,dtrMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22937--22939
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,indMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22939--22941
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22941--22943
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ddenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22943--22945
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 22945--22947
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22947--22949
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22949--22951
[]\T1/pcr/m/n/10 tcrossprod,ldenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22951--22953
[]\T1/pcr/m/n/10 tcrossprod,lgCMatrix,missing-method 
Overfull \hbox (62.8567pt too wide) in paragraph at lines 22953--22955
[]\T1/pcr/m/n/10 tcrossprod,lgeMatrix,diagonalMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 22955--22957
[]\T1/pcr/m/n/10 tcrossprod,lgTMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22957--22959
[]\T1/pcr/m/n/10 tcrossprod,lsparseMatrix,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22961--22963
[]\T1/pcr/m/n/10 tcrossprod,matrix,CsparseMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22963--22965
[]\T1/pcr/m/n/10 tcrossprod,matrix,dgeMatrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 22965--22967
[]\T1/pcr/m/n/10 tcrossprod,matrix,diagonalMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22967--22969
[]\T1/pcr/m/n/10 tcrossprod,matrix,dsCMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22969--22971
[]\T1/pcr/m/n/10 tcrossprod,matrix,dtrMatrix-method 
[3680]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22971--22973
[]\T1/pcr/m/n/10 tcrossprod,Matrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22973--22975
[]\T1/pcr/m/n/10 tcrossprod,matrix,indMatrix-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22975--22977
[]\T1/pcr/m/n/10 tcrossprod,matrix,lsCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22983--22985
[]\T1/pcr/m/n/10 tcrossprod,Matrix,missing-method 
Overfull \hbox (14.8567pt too wide) in paragraph at lines 22985--22987
[]\T1/pcr/m/n/10 tcrossprod,matrix,nsCMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22987--22989
[]\T1/pcr/m/n/10 tcrossprod,Matrix,numLike-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22989--22991
[]\T1/pcr/m/n/10 tcrossprod,Matrix,pMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 22991--22993
[]\T1/pcr/m/n/10 tcrossprod,matrix,pMatrix-method 
Overfull \hbox (50.8567pt too wide) in paragraph at lines 22993--22995
[]\T1/pcr/m/n/10 tcrossprod,Matrix,symmetricMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22995--22997
[]\T1/pcr/m/n/10 tcrossprod,Matrix,TsparseMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 22997--22999
[]\T1/pcr/m/n/10 tcrossprod,mMatrix,sparseVector-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 22999--23001
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ddenseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23001--23003
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ldenseMatrix-method 
Overfull \hbox (32.8567pt too wide) in paragraph at lines 23003--23005
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23005--23007
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,missing-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23007--23009
[]\T1/pcr/m/n/10 tcrossprod,ndenseMatrix,ndenseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23009--23011
[]\T1/pcr/m/n/10 tcrossprod,ngCMatrix,missing-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23011--23013
[]\T1/pcr/m/n/10 tcrossprod,ngTMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23013--23015
[]\T1/pcr/m/n/10 tcrossprod,nsparseMatrix,missing-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23015--23017
[]\T1/pcr/m/n/10 tcrossprod,numLike,CsparseMatrix-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23017--23019
[]\T1/pcr/m/n/10 tcrossprod,numLike,dgeMatrix-method 
Overfull \hbox (2.8567pt too wide) in paragraph at lines 23019--23021
[]\T1/pcr/m/n/10 tcrossprod,numLike,Matrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23021--23023
[]\T1/pcr/m/n/10 tcrossprod,numLike,sparseVector-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 23023--23025
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,missing-method 
Overfull \hbox (8.8567pt too wide) in paragraph at lines 23025--23027
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,pMatrix-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 23027--23029
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,diagonalMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23029--23031
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,sparseVector-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23031--23033
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,missing-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23033--23035
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,mMatrix-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23035--23037
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,numLike-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23037--23039
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseMatrix-method 
Overfull \hbox (68.8567pt too wide) in paragraph at lines 23039--23041
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseVector-method 
Overfull \hbox (20.8567pt too wide) in paragraph at lines 23041--23043
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,ANY-method 
Overfull \hbox (38.8567pt too wide) in paragraph at lines 23043--23045
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,Matrix-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 23045--23047
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,missing-method 
Overfull \hbox (80.8567pt too wide) in paragraph at lines 23047--23049
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,TsparseMatrix-method 
Overfull \hbox (4.01662pt too wide) in paragraph at lines 23090--23092
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 tensor.prod.model.matrix\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3681] [3682] [3683] [3684]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 23729--23731
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3685] [3686] [3687]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 24388--24390
[]\T1/pcr/m/n/10 updown,character,mMatrix,CHMfactor-method 
Overfull \hbox (44.8567pt too wide) in paragraph at lines 24390--24392
[]\T1/pcr/m/n/10 updown,logical,mMatrix,CHMfactor-method 
[3688] [3689]
Underfull \vbox (badness 2285) has occurred while \output is active [3690]
[3691] [3692]) (./fullrefman.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one
pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts
/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/c
ourier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmri8a.pfb>
Output written on fullrefman.pdf (3743 pages, 10277770 bytes).
Transcript written on fullrefman.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh
are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] [-1] Chapter 1
Cross reference values unknown; you must run TeX again. Chapter 2 [1] [2]
[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16]
[17] Chapter 4 [18] Chapter 5 [19] [20] [21] [22] [23] Chapter 6 [24] [25]
Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
[39] [40]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (49 pages, 356724 bytes).
Transcript written on R-FAQ.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux)
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh
are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./R-FAQ.toc [-1]
[-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4]
[5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
Chapter 4 [18] Chapter 5 [19] [20] [21] [22] [23] Chapter 6 [24] [25]
Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
[39] [40]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (51 pages, 372986 bytes).
Transcript written on R-FAQ.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux)
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh
are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./R-FAQ.toc [-1]
[-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4]
[5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
Chapter 4 [18] Chapter 5 [19] [20] [21] [22] [23] Chapter 6 [24] [25]
Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
[39] [40]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (51 pages, 372988 bytes).
Transcript written on R-FAQ.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] Chapter 1 [1] Chapter 2 [2]
Cross reference values unknown; you must run TeX again. [3] [4] [5] [6]
[7] [8] [9] [10] [11] [12] Chapter 3 [13] [14]
Underfull \hbox (badness 7685) in paragraph at lines 1322--1326
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[15] [16] [17] [18] Chapter 4 [19] [20]
Underfull \hbox (badness 10000) in paragraph at lines 1917--1929
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A
[38] [39]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 3371--3371
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
Appendix C [53] [54] [55] [56] [57]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 4985--4985
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 
Overfull \hbox (50.80455pt too wide) in paragraph at lines 4992--4992
 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s
dk/usr/include"[] 
[58]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 5096--5096
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[59]
Overfull \hbox (85.29668pt too wide) in paragraph at lines 5133--5133
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[60] [61] [62] [63] [64]
Overfull \hbox (119.7888pt too wide) in paragraph at lines 5578--5578
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 
[65] [66] Appendix D [67] [68] [69] (Function and variable index) [70]
(Concept index) [71] (Environment variable index) [72] [73] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-admin.pdf (76 pages, 470039 bytes).
Transcript written on R-admin.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-admin.aux) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc)
Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
Chapter 3 [13] [14]
Underfull \hbox (badness 7685) in paragraph at lines 1322--1326
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[15] [16] [17] [18] Chapter 4 [19] [20]
Underfull \hbox (badness 10000) in paragraph at lines 1917--1929
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A
[38] [39]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 3371--3371
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
Appendix C [53] [54] [55] [56] [57]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 4985--4985
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 
Overfull \hbox (50.80455pt too wide) in paragraph at lines 4992--4992
 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s
dk/usr/include"[] 
[58]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 5096--5096
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[59]
Overfull \hbox (85.29668pt too wide) in paragraph at lines 5133--5133
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[60] [61] [62] [63] [64]
Overfull \hbox (119.7888pt too wide) in paragraph at lines 5578--5578
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 
[65] [66] Appendix D [67] [68] [69] (Function and variable index) [70]
(./R-admin.vrs) (Concept index) [71] (./R-admin.cps)
(Environment variable index) [72] (./R-admin.ens) [73] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt9.pfb>
Output written on R-admin.pdf (78 pages, 515426 bytes).
Transcript written on R-admin.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-admin.aux) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc)
Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
Chapter 3 [13] [14]
Underfull \hbox (badness 7685) in paragraph at lines 1322--1326
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[15] [16] [17] [18] Chapter 4 [19] [20]
Underfull \hbox (badness 10000) in paragraph at lines 1917--1929
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A
[38] [39]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 3371--3371
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
Appendix C [53] [54] [55] [56] [57]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 4985--4985
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 
Overfull \hbox (50.80455pt too wide) in paragraph at lines 4992--4992
 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s
dk/usr/include"[] 
[58]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 5096--5096
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[59]
Overfull \hbox (85.29668pt too wide) in paragraph at lines 5133--5133
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[60] [61] [62] [63] [64]
Overfull \hbox (119.7888pt too wide) in paragraph at lines 5578--5578
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 
[65] [66] Appendix D [67] [68] [69] (Function and variable index) [70]
(./R-admin.vrs) (Concept index) [71] (./R-admin.cps)
(Environment variable index) [72] (./R-admin.ens) [73] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt9.pfb>
Output written on R-admin.pdf (78 pages, 515426 bytes).
Transcript written on R-admin.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] (Acknowledgements)
Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls[][]| 
Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2]
[3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4
[13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21]
[22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
(Function and variable index) [28] (Concept index) [29] [30] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (33 pages, 264236 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls[][]| 
Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11]
[12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20]
Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
(Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (35 pages, 303955 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls[][]| 
Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11]
[12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20]
Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
(Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (35 pages, 303965 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls[][]| 
Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11]
[12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20]
Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
(Function and variable index) [28] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (35 pages, 303965 bytes).
Transcript written on R-data.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] (Acknowledgements) Chapter 1 [1]
Cross reference values unknown; you must run TeX again. [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[26] [27] [28]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[29] [30]
Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49] [50] [51] [52]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73]
[74] [75] [76] [77]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 7100--7106
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
Underfull \hbox (badness 10000) in paragraph at lines 8395--8404
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[97] [98] [99]
Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[100] [101]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
Underfull \hbox (badness 10000) in paragraph at lines 8832--8834
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[102]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113]
[114] [115] [116]
Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[117] [118] [119] [120] [121] [122]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[123] [124] [125] [126] [127] [128] [129] [130] [131] [132]
Underfull \hbox (badness 10000) in paragraph at lines 11534--11536
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
[145]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[146] [147] Chapter 6 [148] [149] [150] [151] [152] [153] [154] [155] [156]
[157] [158] [159] [160] Warning: unbalanced parentheses in @def... [161]
[162] [163] [164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 14383--14389
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [167] [168] Chapter 8 [169] [170] [171]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[172]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[173] [174] [175] [176] [177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 15357--15364
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[179] [180] (Function and variable index) [181] (Concept index) [182] [183] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></us
r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-exts.pdf (186 pages, 900223 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[26] [27] [28]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[29] [30]
Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49] [50] [51] [52]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73]
[74] [75] [76] [77]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 7100--7106
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
Underfull \hbox (badness 10000) in paragraph at lines 8395--8404
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[97] [98] [99]
Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[100]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
[101]
Underfull \hbox (badness 10000) in paragraph at lines 8832--8834
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[102]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113]
[114] [115] [116]
Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[117] [118] [119] [120] [121] [122]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[123] [124] [125] [126] [127] [128] [129] [130] [131] [132]
Underfull \hbox (badness 10000) in paragraph at lines 11534--11536
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
[145]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[146] [147] Chapter 6 [148] [149] [150] [151] [152] [153] [154] [155] [156]
[157] [158] [159] [160] Warning: unbalanced parentheses in @def... [161]
[162] [163] [164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 14383--14389
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [167] [168] Chapter 8 [169] [170] [171]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[172]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[173] [174] [175] [176] [177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 15357--15364
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[179] [180] (Function and variable index) [181] (./R-exts.vrs [182] [183])
(Concept index) [184] (./R-exts.cps [185]) [186] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-exts.pdf (192 pages, 964345 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[26] [27] [28]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[29] [30]
Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49] [50] [51] [52]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73]
[74] [75] [76] [77]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 7100--7106
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
Underfull \hbox (badness 10000) in paragraph at lines 8395--8404
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[97] [98] [99]
Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[100]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
[101]
Underfull \hbox (badness 10000) in paragraph at lines 8832--8834
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[102]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113]
[114] [115] [116]
Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[117] [118] [119] [120] [121] [122]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[123] [124] [125] [126] [127] [128] [129] [130] [131] [132]
Underfull \hbox (badness 10000) in paragraph at lines 11534--11536
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
[145]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[146] [147] Chapter 6 [148] [149] [150] [151] [152] [153] [154] [155] [156]
[157] [158] [159] [160] Warning: unbalanced parentheses in @def... [161]
[162] [163] [164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 14383--14389
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [167] [168] Chapter 8 [169] [170] [171]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[172]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[173] [174] [175] [176] [177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 15357--15364
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[179] [180] (Function and variable index) [181] (./R-exts.vrs [182] [183])
(Concept index) [184] (./R-exts.cps [185]) [186] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-exts.pdf (192 pages, 964277 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[26] [27] [28]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[29] [30]
Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49] [50] [51] [52]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73]
[74] [75] [76] [77]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 7100--7106
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91]
Chapter 4 [92] [93] [94] [95] [96]
Underfull \hbox (badness 10000) in paragraph at lines 8395--8404
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[97] [98] [99]
Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[100]
Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
[101]
Underfull \hbox (badness 10000) in paragraph at lines 8832--8834
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[102]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113]
[114] [115] [116]
Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[117] [118] [119] [120] [121] [122]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[123] [124] [125] [126] [127] [128] [129] [130] [131] [132]
Underfull \hbox (badness 10000) in paragraph at lines 11534--11536
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
[145]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[146] [147] Chapter 6 [148] [149] [150] [151] [152] [153] [154] [155] [156]
[157] [158] [159] [160] Warning: unbalanced parentheses in @def... [161]
[162] [163] [164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 14383--14389
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [167] [168] Chapter 8 [169] [170] [171]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[172]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[173] [174] [175] [176] [177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 15357--15364
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[179] [180] (Function and variable index) [181] (./R-exts.vrs [182] [183])
(Concept index) [184] (./R-exts.cps [185]) [186] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-exts.pdf (192 pages, 964277 bytes).
Transcript written on R-exts.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again.
Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3
[12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22]
[23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8
[32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf>
[35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41]
[42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54]
[55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67]
[68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73]
[74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93] Appendix E [94] Appendix F [95]
[96] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/
public/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-intro.pdf (99 pages, 586383 bytes).
Transcript written on R-intro.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-intro.aux) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc)
(Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11]
Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20]
[21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31]
Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p
df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10
[41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53]
[54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66]
[67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72]
[73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93] (./R-intro.vrs [94] [95]) Appendix E
[96] (./R-intro.cps [97]) Appendix F [98] [99] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/
public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public
/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-intro.pdf (105 pages, 637239 bytes).
Transcript written on R-intro.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-intro.aux) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc)
(Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11]
Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20]
[21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31]
Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p
df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10
[41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53]
[54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66]
[67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72]
[73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93] (./R-intro.vrs [94] [95]) Appendix E
[96] (./R-intro.cps [97]) Appendix F [98] [99] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/
public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public
/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-intro.pdf (105 pages, 637235 bytes).
Transcript written on R-intro.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
[13] [14] [15]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52]
Underfull \hbox (badness 7326) in paragraph at lines 4254--4260
 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @
texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] (Concept index) [62] [63] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/cm-super/sfrm1095.pfb>
Output written on R-ints.pdf (66 pages, 405001 bytes).
Transcript written on R-ints.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-ints.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52]
Underfull \hbox (badness 7326) in paragraph at lines 4254--4260
 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @
texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] (./R-ints.vrs [62])
(Concept index) [63] (./R-ints.cps) [64] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm109
5.pfb>
Output written on R-ints.pdf (68 pages, 455830 bytes).
Transcript written on R-ints.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-ints.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52]
Underfull \hbox (badness 7326) in paragraph at lines 4254--4260
 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @
texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] (./R-ints.vrs [62])
(Concept index) [63] (./R-ints.cps) [64] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm109
5.pfb>
Output written on R-ints.pdf (68 pages, 455824 bytes).
Transcript written on R-ints.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] Chapter 1 Chapter 2 [1] [2]
Cross reference values unknown; you must run TeX again.
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4342--4344
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] (Concept Index)
[52] Appendix A [53] [54] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (57 pages, 327087 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-lang.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1
Chapter 2 [1] [2]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4342--4344
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs
[52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (60 pages, 376094 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-lang.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1
Chapter 2 [1] [2]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4342--4344
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs
[52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (60 pages, 376095 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-lang.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1
Chapter 2 [1] [2]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4342--4344
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs
[52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (60 pages, 376095 bytes).
Transcript written on R-lang.log.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc'
+ make MAKEINFO=texi2any info
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi
R-exts.texi:10199: warning: `.' or `,' must follow @xref, not f
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc'
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-intro.info.utf8 doc/manual/R-intro.info
+ mv doc/manual/R-intro.info.utf8 doc/manual/R-intro.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info
+ mv doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/FAQ.utf8 doc/FAQ
+ mv doc/FAQ.utf8 doc/FAQ
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-admin.info.utf8 doc/manual/R-admin.info
+ mv doc/manual/R-admin.info.utf8 doc/manual/R-admin.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1
+ mv doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.E5nLca
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
++ dirname /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
+ cd R-3.6.0
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.6.0-1.el7.arm install install-info
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/m4'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/m4'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/tools'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/tools'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc'
installing doc ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/man/man1
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/html'
installing doc/html ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/html
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/html'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
installing doc/manual ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/manual
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/manual/images
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/etc'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/etc
installing etc ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/etc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/share'
installing share ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/dictionaries
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/encodings
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/java
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/licenses
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/make
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/Rd
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/Rd/macros
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/sh
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/texmf
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/texmf/bibtex/bib
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/texmf/bibtex/bst
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/texmf/tex/latex
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/share'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/bin
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/scripts'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/include/R
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include/R_ext'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/include/R/R_ext
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include/R_ext'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/blas'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/tre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/tre'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/tzone'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/tzone'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/xdr'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/xdr'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/extra/intl'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra/intl'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/appl'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard  -Wl,-z,relro  -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/pkgconfig
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/exec
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/modules
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules/X11'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/library'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/tests'
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/info
/usr/bin/install -c -m 644 "./dir" "/builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/info"
installing R info pages ...
updating '/usr/share/info/dir' ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.6.0-1.el7.arm install-pdf
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/doc/manual'
+ rm -f /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/info/dir
+ rm -f /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/info/dir.old
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0
+ install -p CAPABILITIES /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0
+ cd src/nmath/standalone
+ make install DESTDIR=/builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
make[1]: Entering directory `/builddir/build/BUILD/R-3.6.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.6.0/src/include'
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/etc/ld.so.conf.d
+ echo /usr/lib/R/lib
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/library
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/rpm/macros.d/
+ install -m0644 /builddir/build/SOURCES/macros.R /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/rpm/macros.d/
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/rpm/
+ install -m0755 /builddir/build/SOURCES/R-make-search-index.sh /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/rpm/
+ touch -r README /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/CAPABILITIES
+ touch -r README doc/manual/R-FAQ.pdf doc/manual/R-admin.pdf doc/manual/R-data.pdf doc/manual/R-exts.pdf doc/manual/R-intro.pdf doc/manual/R-ints.pdf doc/manual/R-lang.pdf doc/manual/fullrefman.pdf
+ touch -r README /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/bin/R
+ sed -i 's|\..\/\..|/usr/lib/R|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/html/packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/bkde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/bkde2D.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/bkfe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/dpih.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/dpik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/dpill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/html/locpoly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Aids2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Boston.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Cars93.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Cushings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/DDT.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/GAGurine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Insurance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/MASS-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/OME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Pima.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Rabbit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Rubber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/SP500.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Sitka.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Sitka89.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Skye.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/Traffic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/UScereal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/UScrime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/VA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/abbey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/accdeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/addterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/anorexia.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/anova.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/area.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/bacteria.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/bandwidth.nrd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/bcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/beav1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/beav2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/biopsy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/birthwt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/boxcox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cabbages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/caith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cement.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/chem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/con2tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/contr.sdif.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/coop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/corresp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cov.rob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cov.trob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/cpus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/crabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/deaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/denumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/dose.p.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/drivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/dropterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/eagles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/epil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/eqscplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/farms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/fgl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/fitdistr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/forbes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/fractions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/galaxies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/gamma.dispersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/gamma.shape.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/gehan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/genotype.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/geyser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/gilgais.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/ginv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/glm.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/glm.nb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/hills.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/hist.scott.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/housing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/huber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/hubers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/immer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/isoMDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/kde2d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/ldahist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/leuk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/lm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/lm.ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/loglm1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/logtrans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/mammals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/mcycle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/menarche.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/michelson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/minn38.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/motors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/mvrnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/negative.binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/newcomb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/nlschools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/npr1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/painters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/pairs.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/parcoord.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/petrol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/phones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/plot.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/plot.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/plot.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/polr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/predict.glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/predict.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/predict.lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/predict.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/predict.qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/profile.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/quine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/rational.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/renumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/rms.curv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/rnegbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/road.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/rotifer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/sammon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/ships.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/shoes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/shrimp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/shuttle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/snails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/stdres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/steam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/stepAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/stormer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/studres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/summary.loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/summary.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/summary.rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/survey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/synth.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/theta.md.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/topo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/truehist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/ucv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/waders.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/whiteside.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/width.SJ.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/write.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/html/wtloss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/BunchKaufman-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/CAex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/CHMfactor-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Cholesky-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Cholesky.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/CsparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Diagonal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Hilbert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/KNex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/KhatriRao.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/LU-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Matrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/MatrixClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/MatrixFactorization-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/RsparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Schur-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Schur.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/SparseM-conv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Subassign-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/TsparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/USCounties.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/Xtrct-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/abIndex-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/abIseq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/all-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/all.equal-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/atomicVector-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/band.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/bandSparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/bdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/boolean-matprod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/cBind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/chol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/chol2inv-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/colSums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/compMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/condest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ddenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ddiMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/denseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dgCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dgRMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dgTMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dgeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/diagU2N.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/diagonalMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dpoMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/drop0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dsCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dsRMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dsparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dtCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dtRMatrix-class-def.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dtpMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/dtrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/expm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/externalFormats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/facmul.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/forceSymmetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/formatSparseM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/generalMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/graph2T.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/image-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/indMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/index-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/invPerm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/is.na-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/is.null.DN.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/isSymmetric-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/isTriangular.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/kronecker-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ldenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ldiMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/lgeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/lsparseMatrix-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/lsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ltrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/lu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/matrix-products.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/nMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ndenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/nearPD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ngeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/nnzero.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/nsparseMatrix-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/nsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/ntrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/number-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/pMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/printSpMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/qr-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/rankMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/rcond.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/rep2abI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/replValue-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/rleDiff-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/rsparsematrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/solve-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/spMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparse.model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseLU-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseQR-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseVector-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/sparseVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/symmetricMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/symmpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/triangularMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/uniqTsparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/unpack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/unused-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/html/updown.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Arithmetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/AsIs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Bessel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/CallExternal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Comparison.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Constants.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Cstack_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/DateTimeClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Dates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Encoding.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/EnvVar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Extract.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Extract.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Extremes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Foreign-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Hyperbolic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ISOdatetime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/InternalMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/La_library.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/La_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Last.value.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Log.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Logic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/LongVectors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/MathFun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Memory-limits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Memory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/NA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/NULL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/NumericConstants.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Ops.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Paren.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Platform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Primitive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Quotes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Random-user.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Random.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/RdUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Recall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Reserved.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Rhome.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Round.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Signals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Special.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Startup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Syntax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.getenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.getpid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.glob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.localeconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.readlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.setFileTime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.setenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Sys.which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Trig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/UseMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Vectorize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/Version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/abbreviate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/agrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/all.equal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/all.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/allnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/any.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/aperm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/append.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/apply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/args.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/as.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/as.POSIXlt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/as.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/as.environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/as.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/asplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/assign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/assignOps.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/attach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/attr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/attributes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/autoload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/backsolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/base-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/base-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/base-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/base-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/basename.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/bincode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/bindenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/bitwise.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/body.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/bquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/browser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/browserText.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/builtins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/by.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/callCC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/cat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/cbind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/char.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/character.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/charmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/chartr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/chkDots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/chol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/chol2inv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/col.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/colSums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/colnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/commandArgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/comment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/complex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/conditions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/conflicts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/connections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/contributors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/copyright.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/crossprod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/cumsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/curlGetHeaders.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/cut.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/cut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/data.class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/data.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dataframeHelpers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dcf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/debug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/delayedAssign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/deparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/deparseOpts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/det.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/detach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/diff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/difftime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dimnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/do.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dontCheck.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/double.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dput.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/drop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/droplevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dump.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/duplicated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/dynload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/eapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/eigen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/encodeString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/eval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/exists.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/expand.grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/expression.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/extSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/file.access.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/file.choose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/file.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/file.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/file.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/files2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/find.package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/findInterval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/forceAndCall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/formals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/format.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/format.pval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/formatDL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/formatc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/funprog.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gctorture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/getCallingDLL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/getDLLRegisteredRoutines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/getLoadedDLLs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/getNativeSymbolInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/getwd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/grepRaw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/grouping.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/gzcon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/hexmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/iconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/icuSetCollate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/identical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/identity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ifelse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/integer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/invisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.finite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.language.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.recursive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.single.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/is.unsorted.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/isR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/isS4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/isSymmetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/jitter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/kappa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/kronecker.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/l10n_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/labels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/lapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/lazyload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/lengths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/levels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/libPaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/libcurlVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/library.dynam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/library.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/license.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/list.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/list2env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/locales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/logical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/lower.tri.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/make.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/make.unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/mapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/margin.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/mat.or.vec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/match.arg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/match.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/match.fun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/match.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/matmult.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/maxCol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/memCompress.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/memlimits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/memory.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/merge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/message.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/missing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/mode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/nargs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/nchar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/nlevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/noquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/normalizePath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/notyet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/nrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-dblcolon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-hooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-reflect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/ns-topenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/numeric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/numeric_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/octmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/on.exit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/order.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/parse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/paste.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/path.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/pcre_config.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/pmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/polyroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/pos.to.env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/print.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/print.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/prmatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/proc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/prod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/prop.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/pushBack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/qr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/qraux.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/quit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/range.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/raw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rawConnection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rawConversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readBin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readChar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readRDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readRenviron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/readline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/reg.finalizer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/regex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/regmatches.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/replace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/round.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/row.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/row.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/rowsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sample.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/save.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/scan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/seek.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/seq.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/seq.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/seq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sequence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/serialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/setTimeLimit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/shQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/showConnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/slice.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/slotOp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/socketSelect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/solve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sort.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/split.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sprintf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/srcfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/standardGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/startsWith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/stop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/stopifnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strptime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strsplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strtoi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strtrim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/structure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/strwrap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/subset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/substitute.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/substr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/svd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sweep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/switch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sys.parent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/sys.source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/system.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/system.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/system.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/system2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/t.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/tabulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/tapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/taskCallback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/taskCallbackManager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/taskCallbackNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/tempfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/textconnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/tilde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/timezones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/toString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/trace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/traceback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/tracemem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/transform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/trimws.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/try.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/typeof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/unlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/unlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/unname.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/userhooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/utf8Conversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/validUTF8.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/vector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/warning.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/warnings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/weekday.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/which.min.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/with.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/withVisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/write.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/writeLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/xtfrm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/zMachine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/zScript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/zapsmall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/zpackages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/base/html/zutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/EEF.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/Imp.Estimates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/abc.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/acme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/aids.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/aircondit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/amis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/beaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/bigcity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/boot-practicals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/boot.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/boot.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/brambles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/breslow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/calcium.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cane.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/capability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/catsM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cav.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cd4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cd4.nested.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/censboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/channing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/claridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cloth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/co.transfer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/coal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/corr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cum3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/cv.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/darwin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/dogs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/downs.bc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/ducks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/empinf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/envelope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/exp.tilt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/fir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/freq.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/frets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/glm.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/glm.diag.plots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/gravity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/hirose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/imp.weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/inv.logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/islay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/jack.after.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/k3.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/linear.approx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/lines.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/manaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/motor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/neuro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/nitrofen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/nodal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/norm.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/nuclear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/paulsen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/plot.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/poisons.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/polar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/print.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/print.bootci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/print.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/print.simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/remission.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/saddle.distn.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/saddle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/salinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/simplex.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/smooth.f.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/sunspot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/survival.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/tau.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/tilt.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/tsboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/tuna.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/urine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/var.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/boot/html/wool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/SOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/batchSOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/condense.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/knn.cv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/knn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/knn1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/lvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/lvq2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/lvq3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/lvqinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/lvqtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/multiedit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/olvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/reduce.nn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/html/somgrid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/agnes.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/agriculture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/bannerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/chorSub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/clara.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/clusGap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/clusplot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/clusplot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/cluster-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/coef.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/daisy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/dissimilarity.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/ellipsoidhull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/fanny.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/flower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/lower.to.upper.tri.inds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/mona.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/pam.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/partition.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/plantTraits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/plot.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/plot.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/plot.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/plot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/pltree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/pluton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/predict.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.dissimilarity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/print.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/ruspini.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/silhouette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/sizeDiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/summary.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/summary.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/summary.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/summary.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/summary.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/twins.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/volume.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/votes.repub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/html/xclara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/codetools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/codetools/html/checkUsage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/codetools/html/codetools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/codetools/html/findGlobals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/codetools/html/showTree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/compiler/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/compiler/html/compile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/AirPassengers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/BJsales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/BOD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/ChickWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/DNase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/EuStockMarkets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Formaldehyde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/HairEyeColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Harman23.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Harman74.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Indometh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/InsectSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/JohnsonJohnson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/LakeHuron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/LifeCycleSavings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Loblolly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Nile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Orange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/OrchardSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/PlantGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Puromycin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Theoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/Titanic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/ToothGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/UCBAdmissions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/UKDriverDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/UKLungDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/UKgas.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/USAccDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/USArrests.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/USJudgeRatings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/USPersonalExpenditure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/VADeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/WWWusage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/WorldPhones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/ability.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/airmiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/airquality.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/anscombe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/attenu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/attitude.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/austres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/beavers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/cars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/chickwts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/co2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/crimtab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/datasets-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/discoveries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/esoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/euro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/eurodist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/faithful.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/freeny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/infert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/iris.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/islands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/lh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/longley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/lynx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/morley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/mtcars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/nhtemp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/nottem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/occupationalStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/precip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/presidents.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/pressure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/quakes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/randu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/rivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/rock.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/stackloss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/state.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/sunspot.month.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/sunspot.year.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/sunspots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/swiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/treering.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/trees.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/uspop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/volcano.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/warpbreaks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/women.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/datasets/html/zCO2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/lookup.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.S.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.epiinfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.mtp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.octave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.spss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.ssd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.systat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/read.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/write.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/write.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/write.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/html/write.foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/Devices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/Hershey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/Japanese.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/Type1Font.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/adjustcolor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/as.graphicsAnnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/as.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/axisTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/boxplot.stats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/bringToTop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/cairo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/check.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/chull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/cm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/col2rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/colorRamp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/contourLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/convertColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/densCols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.capture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.flush.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/dev2bitmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/devAskNewPage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/embedFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/extendrange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/getGraphicsEvent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/grDevices-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/grSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/gray.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/gray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/hcl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/make.rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/msgWindow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/n2mfrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/nclass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/palette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/palettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/pdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/pdf.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/pictex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/plotmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/png.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/postscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/postscriptFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/pretty.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/ps.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/quartz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/quartzFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/recordGraphics.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/recordplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/rgb2hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/savePlot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/trans3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/windows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/windows.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/windowsFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/x11.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/x11Fonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/xfig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/xy.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/xyTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/html/xyz.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/abline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/arrows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/assocplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/axTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/axis.POSIXct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/barplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/box.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/boxplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/boxplot.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/bxp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/cdplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/convertXY.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/coplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/dotchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/filled.contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/fourfoldplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/graphics-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/graphics-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/hist.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/hist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/identify.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/image.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/matplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/mosaicplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/mtext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/panel.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/par.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/persp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/pie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.design.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plot.xy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/plothistogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/polypath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/rasterImage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/rug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/screen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/spineplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/stars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/stem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/stripchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/strwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/sunflowerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/symbols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/title.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/units.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/html/zAxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/Grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/absolute.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/arrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/calcStringMetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/current.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/dataViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/depth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/deviceLoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/drawDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/editDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/explode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/gEdit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/gPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/getNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/gpar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.DLapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.add.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.bezier.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.cap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.circle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.copy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.delay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.display.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.draw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.grab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.grill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.grob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.move.to.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.newpage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.pack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.place.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.plot.and.legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.record.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.refresh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.remove.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.reorder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.roundrect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.set.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.show.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.show.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.xaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grid.yaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grobCoords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grobName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grobWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/grobX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/legendGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/makeContent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/plotViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/resolveRasterSize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/showGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/showViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/stringWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/unit.c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/unit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/unit.length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/unit.pmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/unit.rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/valid.just.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/validDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/viewports.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/vpPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/widthDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/xDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/html/xsplinePoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/Lattice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/Rows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/USMortality.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/axis.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/banking.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/barchart.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/barley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/draw.colorkey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/draw.key.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/environmental.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/ethanol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/lattice.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/latticeParseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/level.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/llines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/lset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/make.groups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/oneway.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/packet.panel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.barchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.bwplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.densityplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.dotplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.number.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.qqmathline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.stripplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.superpose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.violin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/panel.xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/prepanel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/prepanel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/print.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/qq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/rfs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/shingles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/simpleKey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/simpleTheme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/singer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/splom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/strip.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/tmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/trellis.device.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/trellis.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/trellis.par.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/update.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/utilities.3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/html/xyplot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/BasicClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Classes_Details.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Documentation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/EmptyMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/EnvironmentClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/GenericFunctions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Introduction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/LanguageClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/LinearMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/MethodDefinition-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/MethodSupport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/MethodWithNext-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/MethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/MethodsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Methods_Details.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Methods_for_Nongenerics.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/Methods_for_S3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/NextMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/ObjectsWithPackage-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/RClassUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/RMethodUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/S3Part.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/S4groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/SClassExtension-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/StructureClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/TraceClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/as.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/callGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/canCoerce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/cbind2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/className.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/classRepresentation-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/classesToAM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/dotsMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/evalSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/findClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/findMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/fixPrevious.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/genericFunction-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/getClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/getMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/getPackageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/hasArg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/implicitGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/inheritedSlotNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/initialize-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/is.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/isSealedMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/languageEl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/localRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/method.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/methodUtilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/methods-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/methods-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/methods-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/new.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/nonStructure-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/promptClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/promptMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/refClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/removeMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/representation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/selectSuperClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setAs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setClassUnion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setGroupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setIs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setLoadActions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setOldClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/setSClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/showMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/signature-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/slot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/stdRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/substituteDirect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/testInheritedMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/validObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/html/zBasicFunsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/FFdes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.cr.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.soap.film.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Rrank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Sl.initial.repara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Sl.repara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Sl.setup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/Tweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/anova.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/bam.update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/bandchol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/bug.reports.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/cSplineDes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/chol.down.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/choose.k.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/columb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/concurvity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/coxpht.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/dDeta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/exclude.too.far.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/extract.lme.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/family.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/fix.family.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/fixDependence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/formXtViX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/formula.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/fs.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/full.score.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.check.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.convergence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.fit3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.fit5.post.proc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.models.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.reparam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.selection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.side.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam.vcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gam2objective.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gamObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gamSim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gamlss.etamu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gamlss.gH.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gamm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gaulss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/get.var.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/gevlss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ginla.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/identifiability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/in.out.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/inSide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/influence.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/initial.sp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/interpret.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/jagam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/k.check.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ldTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ldetS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/linear.functional.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/logLik.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ls.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/magic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/magic.post.proc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mgcv-FAQ.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mgcv-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mgcv-parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mini.roots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/missing.data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/model.matrix.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mono.con.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/mvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/new.name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/notExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/notExp2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/null.space.dimension.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ocat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/one.se.rule.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/pcls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/pdIdnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/pdTens.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/pen.edf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/place.knots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/plot.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/polys.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/predict.bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/predict.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/print.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/qq.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/rTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/residuals.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/rig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/rmvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/s.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/scat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/sdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/single.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/slanczos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.bs.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.gp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.re.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.so.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.sos.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.t2.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smooth2random.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/smoothCon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/sp.vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/spasm.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/step.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/summary.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/t2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/te.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/tensor.prod.model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/totalPenaltySpace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/trichol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/trind.generator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/twlss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/uniquecombs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/vcov.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/vis.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ziP.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/html/ziplss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ACF.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ACF.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Alfalfa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Assay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/BodyWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Cefamandole.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Covariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Covariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Dialyzer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Dim.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Dim.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Dim.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Earthquake.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Extract.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Fatigue.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Gasoline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Glucose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Glucose2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Gun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/IGF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Initialize.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/LDEsysMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Machines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/MathAchSchool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/MathAchieve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Meat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Milk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Names.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Names.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Names.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Names.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Nitrendipene.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Orthodont.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Ovary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Oxboys.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Oxide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/PBG.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Phenobarb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Pixel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Quinidine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Rail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/RatPupWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Relaxin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Remifentanil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Soybean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Spruce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Tetracycline1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Tetracycline2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/VarCorr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Variogram.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Wafer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Wheat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/Wheat2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/allCoef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/anova.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/anova.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/as.matrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/as.matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/as.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/asOneFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/asTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/balancedGrouped.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/bdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/coef.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/collapse.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/collapse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/comparePred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corARMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corCAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corFactor.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corMatrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corMatrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/corSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ergoStool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fdHess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fitted.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fixed.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/fixef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/formula.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/formula.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/formula.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getCovariate.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getCovariate.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getCovariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getCovariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getCovariateFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getData.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getData.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getData.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroups.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getGroupsFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getResponse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getResponseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/getVarCov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gls-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/glsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/glsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gnlsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gnlsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/gsummary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/intervals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/intervals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/intervals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/isBalanced.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/isInitialized.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lmList.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lme.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lme.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logDet.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logDet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logDet.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logDet.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/logLik.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/model.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/needUpdate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/needUpdate.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlme.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/nlsList.selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pairs.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pairs.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pairs.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdConstruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdConstruct.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdDiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdFactor.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdLogChol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pdSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/phenoModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.nffGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.nfnGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.nmGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/plot.ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/pooledSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/predict.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/predict.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/predict.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/predict.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/predict.nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/print.summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/print.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/qqnorm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/qqnorm.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/quinModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/recalc.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/recalc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/recalc.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/recalc.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/recalc.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/residuals.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/simulate.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/solve.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/solve.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/splitFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/summary.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/update.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/update.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varComb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varConstPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varFixed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varWeights.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varWeights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/html/varWeights.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/class.ind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/nnet.Hess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/predict.nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/html/which.is.max.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/RngStream.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/children.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/clusterApply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/detectCores.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/makeCluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/mcaffinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/mcfork.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/mclapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/mcparallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/parallel-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/pvec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/html/splitIndices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/car.test.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/car90.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/cu.summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/kyphosis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/labels.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/meanvar.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/na.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/path.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/plot.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/plotcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/post.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/predict.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/print.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/printcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/prune.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/residuals.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rpart-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rpart.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rpart.exp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rpart.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/rsq.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/snip.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/solder.balance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/stagec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/summary.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/text.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/html/xpred.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/Kaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/Kenvl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/Kfn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/Psim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/SSI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/Strauss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/anova.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/correlogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/expcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/ppgetregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/ppinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/pplik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/ppregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/predict.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/prmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/semat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/surf.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/surf.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/trls.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/trmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/html/variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/asVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/backSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/interpSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/ns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/periodicSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/polySpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/predict.bSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/predict.bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/splineDesign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/splineKnots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/splineOrder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/splines-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/html/xyVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/AIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ARMAacf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ARMAtoMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Cauchy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Chisquare.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Exponential.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Fdist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/GammaDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Geometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Hypergeometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/IQR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/KalmanLike.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Logistic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Lognormal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/NLSstAsymptotic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/NLSstClosestX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/NLSstLfAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/NLSstRtAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/NegBinomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Normal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Poisson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSasymp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSasympOff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSasympOrig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSbiexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSfol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSfpl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSgompertz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSlogis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSmicmen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SSweibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/SignRank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/StructTS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/TDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Tukey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/TukeyHSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Uniform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Weibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/Wilcoxon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/acf2AR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/add1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/addmargins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/aggregate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/alias.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/anova.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/anova.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/anova.mlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ansari.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/approxfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ar.ols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/arima.sim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/arima0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/as.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/asOneSidedFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/bandwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/bartlett.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/binom.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/biplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/biplot.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/birthday.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/box.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cancor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/case.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/checkMFClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/chisq.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cmdscale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/complete.cases.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/constrOptim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/contrasts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/convolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cophenetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cor.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cov.wt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cpgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/cutree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/decompose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/delete.response.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/dendrapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/deriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/deviance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/df.residual.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/diffinv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/dist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/dummy.coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ecdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/eff.aovlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/embed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/expand.model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/extractAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/factanal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/factor.scope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/family.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/fft.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/filter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/fisher.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/fitted.values.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/fivenum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/fligner.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/formula.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/friedman.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ftable.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/getInitial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/glm.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/glm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/heatmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/identify.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/influence.measures.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/integrate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/interaction.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/is.empty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/kernapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/kernel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/kmeans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/kruskal.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ks.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ksmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lag.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/line.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/listof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lm.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lmfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/loadings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/loess.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/logLik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/loglin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lowess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ls.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ls.print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/lsfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mad.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mahalanobis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/make.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/makepredictcall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mantelhaen.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mauchly.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mcnemar.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/median.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/medpolish.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/model.extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/model.tables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/monthplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/mood.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/na.action.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/na.contiguous.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/na.fail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nafns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/naprint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nextn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nlminb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nls.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/nobs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/numericDeriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/offset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/oneway.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/optim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/optimize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/order.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/p.adjust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/pairwise.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/pairwise.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/pairwise.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/pairwise.wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/plot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/poisson.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/poly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/power.anova.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/power.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/power.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/power.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/pp.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ppoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/prcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/predict.smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/preplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/print.power.htest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/print.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/printCoefmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/proj.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/prop.trend.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/qqnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/quade.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/quantile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/r2dtable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/rWishart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/read.ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/rect.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/relevel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/reorder.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/reorder.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/replications.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/reshape.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/runmed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/scatter.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/screeplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/sd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/se.contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/setNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/shapiro.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/sigma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/simulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/smoothEnds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/sortedXyData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/spec.ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/spec.pgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/spec.taper.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/spectrum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/splinefun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stat.anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stats-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stats-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stats-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/step.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/stlmethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/summary.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/supsmu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/symnum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/termplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/terms.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/terms.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/toeplitz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ts-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ts.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/ts.union.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/tsSmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/tsdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/tsp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/uniroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/update.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/var.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/varimax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/weighted.mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/weighted.residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/xtabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/html/zC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/coef-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/confint-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/logLik-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/mle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/plot-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/profile-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/profile.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/show-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/stats4-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/summary-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/summary.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/update-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats4/html/vcov-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/Surv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/Survmethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/aeqSurv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/agreg.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/anova.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/attrassign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/basehaz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/bladder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cgd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cgd0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cipoisson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/clogit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/concordance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/concordancefit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/coxph.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/coxph.detail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/coxph.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/coxph.wtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/diabetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/dsurvreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/finegray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/flchain.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/frailty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/heart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/is.ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/kidney.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/levels.Surv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/lines.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/logLik.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/logan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/lung.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/mgus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/mgus2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/model.frame.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/model.matrix.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/myeloid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/neardate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/nwtco.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/ovarian.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/pbc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/pbcseq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/plot.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/plot.cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/plot.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/predict.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/predict.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/print.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/print.summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/print.summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/print.summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/print.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/pspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/pyears.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/quantile.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/ratetableDate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/rats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/rats2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/reliability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/residuals.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/residuals.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/retinopathy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/rhDNase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/solder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/stanford2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/statefig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/strata.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/summary.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/summary.pyears.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survConcordance-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survSplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survexp.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survexp.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survexp.us.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfit.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfit.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfit.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfit.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survfitcoxph.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survival-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survobrien.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survreg.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survreg.distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survreg.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/survregDtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/tcut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/tmerge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/tobin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/transplant.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/udca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/untangle.specials.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/uspop2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/vcov.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/veteran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/xtfrm.Surv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/yates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/html/yates_setup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/TclInterface.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/TkCommands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/TkWidgetcmds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/TkWidgets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tclServiceMode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tcltk-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tcltk-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tkProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tkStartGUI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tk_choose.dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tk_choose.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tk_messageBox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tk_select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/html/tkpager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/CRANtools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/HTMLheader.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/HTMLlinks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/QC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rcmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rd2HTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rd2txt_options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/RdTextFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rdindex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/Rdutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/SweaveTeXFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/add_datalist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/assertCondition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/bibstyle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/buildVignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/buildVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/charsets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkFF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkMD5sums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkPoFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkRdaFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkTnF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/checkVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/check_packages_in_dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/codoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/compactPDF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/delimMatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/dependsOnPkgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/encoded.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/fileutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/find_gs_cmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/getVignetteInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/loadRdMacros.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/makeLazyLoading.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/make_translations_pkg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/makevars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/md5sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/package_dependencies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/package_native_routine_registration_skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/parseLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/parse_Rd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/print.via.format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/pskill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/psnice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/read.00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/showNonASCII.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/startDynamicHelp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/testInstalledPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/texi2dvi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/toHTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/toRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/toTitleCase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/tools-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/tools-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/tools-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/undoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/updatePACKAGES.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/update_pkg_po.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/vignetteEngine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/vignetteInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/writePACKAGES.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/html/xgettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/BATCH.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/COMPILE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/DLL.version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/INSTALL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/LINK.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/PkgUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Question.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/REMOVE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/RHOME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/RShowDoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/RSiteSearch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Rconsole.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Rprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Rprofmem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Rscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Rtangle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/RweaveLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/SHLIB.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/Sweave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/SweaveSyntConv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/SweaveUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/URLencode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/View.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/adist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/alarm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/apropos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/aregexec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/arrangeWindows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/askYesNo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/aspell-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/aspell.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/available.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/bibentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/browseEnv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/browseURL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/browseVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/bug.report.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/capture.output.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/changedFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/choose.dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/choose.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/chooseBioCmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/chooseCRANmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/citEntry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/citation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/cite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/clipboard.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/close.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/combn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/compareVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/contrib.url.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/count.fields.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/create.post.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/dataentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/debugcall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/debugger.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/demo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/download.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/download.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/edit.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/example.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/file.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/filetest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/findLineNum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/fix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/flush.console.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getAnywhere.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getFromNamespace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getParseData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getWindowsHandle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/getWindowsHandles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/glob2rx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/globalVariables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/hasName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/head.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/help.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/help.request.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/help.search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/help.start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/hsearch-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/install.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/installed.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/isS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/isS3stdGen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/localeToCharset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/ls_str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/maintainer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/make.packages.html.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/make.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/memory.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/menu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/mirrorAdmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/modifyList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/news.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/nsl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/object.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/package.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/packageDescription.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/packageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/packageStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/page.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/person.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/process.events.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/prompt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/promptData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/promptPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/rcompgen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/read.DIF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/read.fortran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/read.fwf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/read.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/read.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/readRegistry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/recover.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/relist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/remove.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/removeSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/roman.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/rtags.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/savehistory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/sessionInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/setRepositories.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/setWindowTitle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/shortPathName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/sourceutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/stack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/strcapture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/summaryRprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/tar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/toLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/txtProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/type.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/untar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/unzip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/update.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/url.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/utils-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/utils-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/utils-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/vignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/warnErrList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/winDialog.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/winMenus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/winProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/winextras.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/write.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.6.0|g' /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/html/zip.html
+ chmod +x /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/R/sh/echo.sh
+ chmod +x /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/BATCH /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/COMPILE /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/INSTALL /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/LINK /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/R /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/REMOVE /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rcmd /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rd2pdf /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rdconv /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rdiff /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rprof /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rscript /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/SHLIB /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Stangle /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Sweave /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/build /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/check /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/config /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/exec /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/javareconf /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/libtool /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/mkinstalldirs /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/pager /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/rtags
+ chmod -x /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/CITATION /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/R-3.6.0/CAPABILITIES
~/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R ~/build/BUILD/R-3.6.0
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/include ']'
+ pushd /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R
+ ln -s ../../include/R include
+ popd
~/build/BUILD/R-3.6.0
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/texmf/tex/latex/R ']'
+ mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/texmf/tex/latex
~/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/texmf/tex/latex ~/build/BUILD/R-3.6.0
+ pushd /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/texmf/tex/latex
+ ln -s /usr/share/R/texmf/tex/latex R
~/build/BUILD/R-3.6.0
+ popd
+ mv /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib/libRblas.so /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib/libRrefblas.so
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/R-3.6.0
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/libRmath.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/Rscript
*** WARNING: identical binaries are copied, not linked:
        /usr/lib/R/bin/Rscript
   and  /usr/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/bin/exec/R
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/methods/libs/methods.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grid/libs/grid.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/libs/grDevices.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/grDevices/libs/cairo.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/Matrix/libs/Matrix.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/lattice/libs/lattice.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nlme/libs/nlme.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/nnet/libs/nnet.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/MASS/libs/MASS.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/foreign/libs/foreign.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/class/libs/class.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/KernSmooth/libs/KernSmooth.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/rpart/libs/rpart.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tcltk/libs/tcltk.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/graphics/libs/graphics.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/spatial/libs/spatial.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/splines/libs/splines.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/cluster/libs/cluster.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/stats/libs/stats.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/utils/libs/utils.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/parallel/libs/parallel.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/mgcv/libs/mgcv.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/tools/libs/tools.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/library/survival/libs/survival.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib/libRlapack.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib/libRrefblas.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/lib/libR.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/modules/R_de.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/modules/lapack.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/modules/R_X11.so
extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/lib/R/modules/internet.so
/usr/lib/rpm/sepdebugcrcfix: Updated 35 CRC32s, 0 CRC32s did match.
cpio: R-3.6.0/src/modules/lapack/SRC/iparam2stage.F: Cannot stat: No such file or directory
33611 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.LI2Kmr
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.6.0
Processing files: R-3.6.0-1.el7.armv7hl
Provides: R = 3.6.0-1.el7 R(armv7hl-32) = 3.6.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-core-3.6.0-1.el7.armv7hl
+ exit 0
Provides: R-KernSmooth = 2.23.15 R-MASS = 7.3.51.4 R-Matrix = 1.2.17 R-base = 3.6.0 R-boot = 1.3.22 R-class = 7.3.15 R-cluster = 2.0.8 R-codetools = 0.2.16 R-core = 3.6.0-1.el7 R-core(armv7hl-32) = 3.6.0-1.el7 R-datasets = 3.6.0 R-foreign = 0.8.71 R-grDevices = 3.6.0 R-graphics = 3.6.0 R-grid = 3.6.0 R-lattice = 0.20.38 R-methods = 3.6.0 R-mgcv = 1.8.28 R-nlme = 3.1.139 R-nnet = 7.3.12 R-parallel = 3.6.0 R-rpart = 4.1.15 R-spatial = 7.3.11 R-splines = 3.6.0 R-stats = 3.6.0 R-stats4 = 3.6.0 R-survival = 2.44.1.1 R-tcltk = 3.6.0 R-tools = 3.6.0 R-utils = 3.6.0 config(R-core) = 3.6.0-1.el7 libR.so libRlapack.so libRrefblas.so
Requires(interp): /bin/sh /bin/sh /bin/sh
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /bin/sh
Requires(postun): /bin/sh
Requires(posttrans): /bin/sh
Requires: /bin/bash /bin/sh ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libICE.so.6 libR.so libRblas.so libRlapack.so libSM.so.6 libX11.so.6 libXext.so.6 libXmu.so.6 libXt.so.6 libbz2.so.1 libc.so.6 libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.16) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.6) libc.so.6(GLIBC_2.7) libc.so.6(GLIBC_2.8) libcairo.so.2 libcurl.so.4 libdl.so.2 libdl.so.2(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_3.3.1) libgcc_s.so.1(GCC_3.5) libgfortran.so.3 libgfortran.so.3(GFORTRAN_1.0) libglib-2.0.so.0 libgobject-2.0.so.0 libgomp.so.1 libgomp.so.1(GOMP_1.0) libgomp.so.1(OMP_1.0) libicui18n.so.50 libicuuc.so.50 libjpeg.so.62 libjpeg.so.62(LIBJPEG_6.2) liblzma.so.5 liblzma.so.5(XZ_5.0) libm.so.6 libm.so.6(GLIBC_2.4) libpango-1.0.so.0 libpangocairo-1.0.so.0 libpcre.so.1 libpcre2-8.so.0 libpng15.so.15 libpng15.so.15(PNG15_0) libpthread.so.0 libpthread.so.0(GLIBC_2.4) libreadline.so.6 librt.so.1 librt.so.1(GLIBC_2.4) libtcl8.5.so libtiff.so.5 libtiff.so.5(LIBTIFF_4.0) libtk8.5.so libtre.so.5 libz.so.1 rtld(GNU_HASH)
Obsoletes: R-Matrix < 0.999375-7
Processing files: R-core-devel-3.6.0-1.el7.armv7hl
Provides: R-Matrix-devel = 1.2.17 R-core-devel = 3.6.0-1.el7 R-core-devel(armv7hl-32) = 3.6.0-1.el7 pkgconfig(libR) = 3.6.0
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Obsoletes: R-Matrix-devel < 0.999375-7
Processing files: R-devel-3.6.0-1.el7.armv7hl
Provides: R-devel = 3.6.0-1.el7 R-devel(armv7hl-32) = 3.6.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-java-3.6.0-1.el7.armv7hl
Provides: R-java = 3.6.0-1.el7 R-java(armv7hl-32) = 3.6.0-1.el7
Requires(interp): /bin/sh
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Requires(post): R-core = 3.6.0-1.el7 /bin/sh
Processing files: R-java-devel-3.6.0-1.el7.armv7hl
Provides: R-java-devel = 3.6.0-1.el7 R-java-devel(armv7hl-32) = 3.6.0-1.el7
Requires(interp): /bin/sh
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Requires(post): R-core-devel = 3.6.0-1.el7 java-devel /bin/sh
Processing files: libRmath-3.6.0-1.el7.armv7hl
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3BIdlW
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.6.0
+ DOCDIR=/builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/libRmath-3.6.0
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/libRmath-3.6.0
+ cp -pr doc/COPYING /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm/usr/share/doc/libRmath-3.6.0
+ exit 0
Provides: libRmath = 3.6.0-1.el7 libRmath(armv7hl-32) = 3.6.0-1.el7 libRmath.so
Requires(interp): /sbin/ldconfig /sbin/ldconfig
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /sbin/ldconfig
Requires(postun): /sbin/ldconfig
Requires: ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libgomp.so.1 libm.so.6 libm.so.6(GLIBC_2.4) libpthread.so.0 libpthread.so.0(GLIBC_2.4) rtld(GNU_HASH)
Processing files: libRmath-devel-3.6.0-1.el7.armv7hl
Provides: libRmath-devel = 3.6.0-1.el7 libRmath-devel(armv7hl-32) = 3.6.0-1.el7 pkgconfig(libRmath) = 3.6.0
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Processing files: libRmath-static-3.6.0-1.el7.armv7hl
Provides: libRmath-static = 3.6.0-1.el7 libRmath-static(armv7hl-32) = 3.6.0-1.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-debuginfo-3.6.0-1.el7.armv7hl
Provides: R-debuginfo = 3.6.0-1.el7 R-debuginfo(armv7hl-32) = 3.6.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
Wrote: /builddir/build/RPMS/R-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-core-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-core-devel-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-devel-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-java-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-java-devel-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-devel-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-static-3.6.0-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-debuginfo-3.6.0-1.el7.armv7hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.oUcapf
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.6.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-3.6.0-1.el7.arm
+ exit 0
Child return code was: 0