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-25976e9085064b8676d7c212f59743dd5000d361/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 0x338970>uid=996)
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-3.3.0-3.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-25976e9085064b8676d7c212f59743dd5000d361/root'shell=Falseuid=996env={'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 0x338970>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.W1JoHe
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf R-3.3.0
+ /usr/bin/tar -xf -
+ /usr/bin/gzip -dc /builddir/build/SOURCES/R-3.3.0.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd R-3.3.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (0001-Disable-backing-store-in-X11-window.patch):
+ echo 'Patch #0 (0001-Disable-backing-store-in-X11-window.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/0001-Disable-backing-store-in-X11-window.patch
+ /usr/bin/patch -p1 -b --suffix .disable-backing-store --fuzz=0
patching file src/modules/X11/devX11.c
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
+ cat
+ chmod +x /builddir/build/BUILD/R-3.3.0/R-prov
+ cat
+ chmod +x /builddir/build/BUILD/R-3.3.0/R-req
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.wQ8yVW
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.3.0
+ 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-R-shlib --enable-prebuilt-html MAKEINFO=texi2any rdocdir=/usr/share/doc/R-3.3.0 rincludedir=/usr/include/R rsharedir=/usr/share/R
configure: WARNING: unrecognized options: --disable-dependency-tracking
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-3.3.0/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/m4'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tools'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/html'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/html'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/etc'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/etc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/share'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/share'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include'
mkdir -p -- ../../include
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include/R_ext'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
gfortran  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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-3.3.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
mkdir -p -- /builddir/build/BUILD/R-3.3.0/lib
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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-3.3.0/src/appl'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 expm1.d from expm1.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-3.3.0/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 expm1.c -o expm1.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 expm1.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-3.3.0/src/nmath'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/src/unix'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/unix'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 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-3.3.0/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 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
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
main.c: In function 'dummy_ii':
main.c:1656:5: warning: function returns address of local variable [-Wreturn-local-addr]
     return (uintptr_t) &ii;
     ^
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  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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 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 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/main'
mkdir -p -- /builddir/build/BUILD/R-3.3.0/bin/exec
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/main'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILD/R-3.3.0/modules
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/internet'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/internet'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
making Lapack.d from Lapack.c
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 -ffloat-store -c dlamch.f -o dlamch.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gfortran  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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"
dlapack.f:6851.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:6865.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:9142.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:9757.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:10301.24:
               HSWORK = WORK( 1 )                                       
                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:10310.24:
               HSWORK = WORK( 1 )                                       
                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:10317.24:
               HSWORK = WORK( 1 )                                       
                        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:10957.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15427.28:
               LWORK_DGEQRF=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15431.28:
               LWORK_DORMQR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15446.28:
               LWORK_DGEBRD=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15450.28:
               LWORK_DORMBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:94639.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15454.28:
               LWORK_DORGBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15478.31:
                  LWORK_DGELQF=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15482.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15486.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15490.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15494.31:
                  LWORK_DORMLQ=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15514.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15518.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:15522.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22203.25:
            LWORK_DGEQRF=DUM(1)                                         
                         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22206.27:
            LWORK_DORGQR_N=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22208.27:
            LWORK_DORGQR_M=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22212.25:
            LWORK_DGEBRD=DUM(1)                                         
                         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22216.27:
            LWORK_DORGBR_P=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22220.27:
            LWORK_DORGBR_Q=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22336.28:
               LWORK_DGEBRD=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22341.33:
                  LWORK_DORGBR_Q=DUM(1)                                 
                                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22347.33:
                  LWORK_DORGBR_Q=DUM(1)                                 
                                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22364.25:
            LWORK_DGELQF=DUM(1)                                         
                         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22367.27:
            LWORK_DORGLQ_N=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22369.27:
            LWORK_DORGLQ_M=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22373.25:
            LWORK_DGEBRD=DUM(1)                                         
                         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22377.27:
            LWORK_DORGBR_P=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22381.27:
            LWORK_DORGBR_Q=DUM(1)                                       
                           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22496.28:
               LWORK_DGEBRD=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22502.32:
                 LWORK_DORGBR_P=DUM(1)                                  
                                1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:22508.32:
                 LWORK_DORGBR_P=DUM(1)                                  
                                1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:34180.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:33122.13:
      LOPT = WORK( M+NP+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:34478.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:33826.13:
      LOPT = WORK( P+MN+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:120282.14:
      LWMIN = MAX( DBLE( LWMIN ), DBLE( WORK( 1 ) ) )                   
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:120283.15:
      LIWMIN = MAX( DBLE( LIWMIN ), DBLE( IWORK( 1 ) ) )                
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:132944.13:
      LOPT = MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) )                     
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:132945.14:
      LIOPT = MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) )                  
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:134116.21:
            LWKOPT = WORK(1)                                            
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
dlapack.f:74227.34:
      SUBROUTINE DLARRV( N, VL, VU, D, L, PIVMIN,                       
                                  1
Warning: Unused dummy argument 'vu' at (1)
dlapack.f:70780.54:
      SUBROUTINE DLARRC( JOBT, N, VL, VU, D, E, PIVMIN,                 
                                                      1
Warning: Unused dummy argument 'pivmin' at (1)
dlapack.f:43028.45:
     $                   RELTOL, PIVMIN, D, E, E2, NVAL, AB, C, MOUT,   
                                             1
Warning: Unused dummy argument 'e' at (1)
dlapack.f:55170.55:
      INTEGER FUNCTION DLANEG( N, D, LLD, SIGMA, PIVMIN, R )            
                                                       1
Warning: Unused dummy argument 'pivmin' at (1)
dlapack.f:159644.68:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                                    1
Warning: Unused dummy argument 'lwork' at (1)
dlapack.f:159644.51:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                   1
Warning: Unused dummy argument 'n' at (1)
dlapack.f:159644.48:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                1
Warning: Unused dummy argument 'opts' at (1)
dlapack.f:125049.23:
     $           ABSTOL, M, W, Z, LDZ, ISUPPZ, WORK, LWORK, IWORK,      
                       1
Warning: Unused dummy argument 'abstol' at (1)
dlapack.f: In function 'dlatrs':
dlapack.f:91494:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dlatps':
dlapack.f:90369:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dgghrd':
dlapack.f:33523:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
dlapack.f: In function 'dlatbs':
dlapack.f:89253:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dsptrf':
dlapack.f:122681:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dtptri':
dlapack.f:151073:0: warning: 'jclast' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                     AP( JCLAST ), AP( JC+1 ), 1 )
 ^
dlapack.f: In function 'dlaruv':
dlapack.f:76247:0: warning: 'it4' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 4 ) = IT4
 ^
dlapack.f:76246:0: warning: 'it3' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 3 ) = IT3
 ^
dlapack.f:76245:0: warning: 'it2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 2 ) = IT2
 ^
dlapack.f:76244:0: warning: 'it1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 1 ) = IT1
 ^
dlapack.f: In function 'dstein':
dlapack.f:125476:0: warning: 'xjm' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ABS( XJ-XJM ).GT.ORTOL )
 ^
dlapack.f:125476:0: warning: 'ortol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:125462:0: warning: 'onenrm' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $            ABS( WORK( INDRV1+JMAX ) )
 ^
dlapack.f:125496:0: warning: 'dtpcrt' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( NRM.LT.DTPCRT )
 ^
dlapack.f: In function 'dlaed8':
dlapack.f:47153:0: 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 'dlaed6':
dlapack.f:46469:0: warning: 'sclinv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $   TAU = TAU*SCLINV
 ^
dlapack.f: In function 'dlaed2':
dlapack.f:44309:0: warning: 'pj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   N2, NJ, PJ
 ^
dlapack.f: In function 'dgetc2':
dlapack.f:27800:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          A( N, N ) = SMIN
 ^
dlapack.f:27782:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $      CALL DSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 )
 ^
dlapack.f:27730:0: 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:87583:0: warning: 'jpsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( JPSV.NE.I )
 ^
dlapack.f:87577:0: warning: 'ipsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IPSV.NE.I ) THEN
 ^
dlapack.f: In function 'dtgevc':
dlapack.f:143070:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILBACK ) THEN
 ^
dlapack.f: In function 'dlahqr':
dlapack.f:51887:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DO 100 J = K, I2
 ^
dlapack.f: In function 'dlahr2':
dlapack.f:52273:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
dlapack.f: In function 'dlasd7':
dlapack.f:81535:0: 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:78685:0: 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 'dlasq4':
dlapack.f:85078:0: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       TAU = S
 ^
dlapack.f: In function 'dlals0':
dlapack.f:53770:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
dlapack.f: In function 'dlasd8':
dlapack.f:82129:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   / ( DSIGMA( I )+DJ )
 ^
dlapack.f: In function 'dsytf2':
dlapack.f:135682:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dlange':
dlapack.f:55641:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
dlapack.f: In function 'dtrsen':
dlapack.f:154673:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WORK( 1 ) = LWMIN
 ^
dlapack.f:154674:0: warning: 'liwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IWORK( 1 ) = LIWMIN
 ^
dlapack.f: In function 'dlantr':
dlapack.f:58918:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantp':
dlapack.f:58546:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantb':
dlapack.f:58201:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansy':
dlapack.f:57941:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlanst':
dlapack.f:57733:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM
 ^
dlapack.f: In function 'dlansp':
dlapack.f:57486:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansb':
dlapack.f:56280:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlarrf':
dlapack.f:73036:0: warning: 'indx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF(INDX.EQ.1) THEN
 ^
dlapack.f: In function 'dlanhs':
dlapack.f:56054:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dhgeqz':
dlapack.f:39911:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ ) THEN
 ^
dlapack.f:39402:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
dlapack.f:39625:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( .NOT.ILSCHR ) THEN
 ^
dlapack.f: In function 'dlangt':
dlapack.f:55844:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM, TEMP
 ^
dlapack.f: In function 'dlangb':
dlapack.f:55427:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
dlapack.f: In function 'iparmq':
dlapack.f:159802:0: warning: 'ns' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( NS.GE.KACMIN )
 ^
dlapack.f:159793:0: warning: 'nh' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( NH.GE.K22MIN )
 ^
dlapack.f: In function 'dlaed0':
dlapack.f:43744:0: warning: 'iwrem' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      IWORK( SUBPBS+1 ), INFO )
 ^
dlapack.f:43744:0: warning: 'iqptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:43744:0: warning: 'iq' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:43744:0: warning: 'iprmpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:43744:0: warning: 'iperm' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:43744:0: warning: 'igivpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:43744:0: warning: 'igivcl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormql':
dlapack.f:98936:0: 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:95691:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dsyevx':
dlapack.f:131684:0: warning: 'lwkopt' may be used uninitialized in this function [-Wmaybe-uninitialized]
       WORK( 1 ) = LWKOPT
 ^
dlapack.f: In function 'dlarrd':
dlapack.f:71624:0: warning: 'wul' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( W( JE ).GE.WUL .AND. IDISCU.GT.0 ) THEN
 ^
dlapack.f:71607:0: 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:72132:0: 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:72625:0: warning: 'wend' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WBEGIN = WEND + 1
 ^
dlapack.f:72611:0: 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:100193:0: 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:148277:0: warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCALE = SCALE2
 ^
dlapack.f: In function 'dtgsna':
dlapack.f:146581:0: warning: 'cond' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           COND )
 ^
dlapack.f: In function 'dbdsdc':
dlapack.f:1541:0: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      WORK( WSTART ), IWORK, INFO )
 ^
dlapack.f:1541:0: warning: 'poles' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'ivt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'is' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'ic' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'givnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'givcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'difr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1541:0: warning: 'difl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormrz':
dlapack.f:100564:0: 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:158015:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dgehrd':
dlapack.f:11743:0: 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:5370:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:5385:0: 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:9685:0: warning: 'maxwrk' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   MAXWRK, MINWRK
 ^
dlapack.f: In function 'dgelss':
dlapack.f:15611:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f: In function 'dgesdd':
dlapack.f:20835:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f:20883:0: warning: 'bdspac' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( LWORK.GE.LDA*N+N*N+3*N+BDSPAC ) THEN
 ^
dlapack.f:20519:0: warning: 'il' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            BDSPAC, BLK, CHUNK, I, IE, IERR, IL,
 ^
dlapack.f:20520:0: warning: 'ir' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   IR, ISCL, ITAU, ITAUP, ITAUQ, IU, IVT, LDWKVT,
 ^
dlapack.f: In function 'dgesvd':
dlapack.f:22563:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f:22123:0: warning: 'bdspac' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            BDSPAC, BLK, CHUNK, I, IE, IERR, IR, ISCL,
 ^
dlapack.f:25347:0: warning: 'ie' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IE.LT.2 ) THEN
 ^
dlapack.f:22126:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
dlapack.f: In function 'dgesvx':
dlapack.f:27435:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:27450:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f: In function 'dlansf':
dlapack.f:56618:0: 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:93889:0: warning: 'itauq2' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:93889:0: warning: 'itauq1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93889:0: warning: 'itaup2' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93889:0: warning: 'itaup1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93953:0: warning: 'iorgqr' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGQR), LORGQRWORK, INFO )
 ^
dlapack.f:93935:0: warning: 'iorglq' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGLQ), LORGLQWORK, INFO )
 ^
dlapack.f:93889:0: warning: 'iorbdb' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:93963:0: warning: 'ibbcsd' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IB22E), WORK(IBBCSD), LBBCSDWORK, INFO )
 ^
dlapack.f:93963:0: warning: 'ib22e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib22d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib21e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib21d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib12e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib12d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib11e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:93963:0: warning: 'ib11d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dorgrq':
dlapack.f:96479:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dpbsvx':
dlapack.f:102893:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:102893:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dposvx':
dlapack.f:106774:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:106774:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dppsvx':
dlapack.f:109456:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:109456:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dlahrd':
dlapack.f:163133:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
gfortran  -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_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:2455.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2474.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2499.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2518.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21486.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21526.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21570.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21604.24:
               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:4175.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:50064.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10643.25:
            LWORK_ZGEQRF=CDUM(1)                                        
                         1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10646.27:
            LWORK_ZUNGQR_N=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10648.27:
            LWORK_ZUNGQR_M=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10652.25:
            LWORK_ZGEBRD=CDUM(1)                                        
                         1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10656.27:
            LWORK_ZUNGBR_P=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10659.27:
            LWORK_ZUNGBR_Q=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10766.28:
               LWORK_ZGEBRD=CDUM(1)                                     
                            1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10771.33:
                  LWORK_ZUNGBR_Q=CDUM(1)                                
                                 1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10777.33:
                  LWORK_ZUNGBR_Q=CDUM(1)                                
                                 1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10792.25:
            LWORK_ZGELQF=CDUM(1)                                        
                         1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10796.27:
            LWORK_ZUNGLQ_N=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10798.27:
            LWORK_ZUNGLQ_M=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10802.25:
            LWORK_ZGEBRD=CDUM(1)                                        
                         1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10806.27:
            LWORK_ZUNGBR_P=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10810.27:
            LWORK_ZUNGBR_Q=CDUM(1)                                      
                           1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10916.28:
               LWORK_ZGEBRD=CDUM(1)                                     
                            1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10922.32:
                 LWORK_ZUNGBR_P=CDUM(1)                                 
                                1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:10928.32:
                 LWORK_ZUNGBR_P=CDUM(1)                                 
                                1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:18658.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:37909.26:
               E( I-1 ) = ALPHA                                         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:37963.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19792.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19378.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19406.23:
            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:19409.18:
         D( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19422.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19451.21:
            D( I ) = A( I, I )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19454.18:
         D( N ) = A( N, N )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19824.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19049.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39127.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39146.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39568.18:
            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:39595.18:
            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:1998.29:
      COMPLEX*16         CDUM                                           
                             1
Warning: Unused variable 'cdum' declared at (1)
cmplx.f: In function 'zsyr':
cmplx.f:42001:0: 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:42705:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
cmplx.f: In function 'zlaed8':
cmplx.f:23661:0: 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:27814:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zlanhe':
cmplx.f:27330:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
cmplx.f: In function 'ztgevc':
cmplx.f:44165:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( ILBACK ) THEN
 ^
cmplx.f:44041:0: warning: 'ilall' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILALL ) THEN
 ^
cmplx.f: In function 'zlange':
cmplx.f:27108:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
cmplx.f: In function 'zgetc2':
cmplx.f:14753:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   BIGNUM, EPS, SMIN, SMLNUM, XMAX
 ^
cmplx.f:14804:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $      CALL ZSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 )
 ^
cmplx.f:14752:0: 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:18409:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
cmplx.f: In function 'zlanhs':
cmplx.f:27573:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zhgeqz':
cmplx.f:20694:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ )
 ^
cmplx.f:20636:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
cmplx.f:20542:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( .NOT.ILSCHR ) THEN
 ^
cmplx.f: In function 'zlals0':
cmplx.f:25492:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                            DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
cmplx.f: In function 'zlahqr':
cmplx.f:24412:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                      IF( I2.GT.J )
 ^
cmplx.f: In function 'zlahr2':
cmplx.f:24769:0: warning: 'IMAGPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
cmplx.f:24668:0: warning: 'REALPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       COMPLEX*16        EI
 ^
cmplx.f: In function 'ztgsyl':
cmplx.f:46738:0: warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCALE = SCALE2
 ^
cmplx.f: In function 'ztrsen':
cmplx.f:48183:0: 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:54392:0: 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:51120:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
cmplx.f: In function 'zgehrd':
cmplx.f:4911:0: 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:6397:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f: In function 'zgesvd':
cmplx.f:10982:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f:10565:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
cmplx.f: In function 'zgesvx':
cmplx.f:14456:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
cmplx.f:14471:0: 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:51911:0: 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-3.3.0/src/modules/lapack'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/modules/lapack'
/builddir/build/BUILD/R-3.3.0/lib/libRlapack.so is unchanged
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/modules/X11'
gcc -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -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  -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -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  -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -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  -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -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-3.3.0/src/modules/X11'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules/X11'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/X11'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/X11'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
mkdir -p -- ../../library
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/profile'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/translations'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/translations'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/translations'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
building package 'base'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/compiler'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/utils'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src/cairo'
make[9]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src/cairo'
gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -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-3.3.0/src/library/grDevices/src/cairo'
make[8]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src/cairo'
make[7]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src/cairo'
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grDevices'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/graphics'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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:1853.22:
      logical i1,i2,i3,leaf                                             
                      1
Warning: Unused variable 'i3' declared 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"
ppr.f:1323.8:
      t=a(ij)                                                           
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1328.8:
      t=a(ij)                                                           
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1336.8:
      t=a(ij)                                                           
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1343.8:
      t=a(ij)                                                           
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1354.9:
      tt=a(l)                                                           
         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1379.8:
      t=a(i+1)                                                          
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:370.10:
        k=sc(j,1)                                                       
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1088.10:
      ibw=0.5d0*span*n+0.5d0                                            
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:396.10:
        k=sc(j,1)                                                       
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:404.10:
        k=sc(j,1)                                                       
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:115.8:
      l=sc(lm,1)                                                        
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:844.14:
            k=sp(j,1)                                                   
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:860.8:
      m=smod(1)+0.1d0                                                   
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:861.8:
      p=smod(2)+0.1d0                                                   
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:862.8:
      q=smod(3)+0.1d0                                                   
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:863.8:
      n=smod(4)+0.1d0                                                   
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:864.9:
      mu=smod(5)+0.1d0                                                  
         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
ppr.f:1229.42:
      integer iparms(3), i, nk, ip, isetup,ier                          
                                          1
Warning: Unused variable 'isetup' declared 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 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 -ffloat-store -c portsrc.f -o portsrc.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
portsrc.f: In function 'i7do':
portsrc.f:6428:0: warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
          NCOMP = NCOMP + 1
 ^
portsrc.f:6448:0: warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
          JPU = JPNTR(JCOL+1) - 1
 ^
portsrc.f: In function 'df7dhb':
portsrc.f:12276:0: warning: 'pp1o2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       HPI = HES + PP1O2
 ^
portsrc.f: In function 'dl7mst':
portsrc.f:5328:0: 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:5463:0: 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:10090:0: warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
 ^
portsrc.f:10008:0: 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:10003:0: warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
       LK = DMAX1(LK, PHI*W(PHIPIN))
 ^
portsrc.f:10144:0: 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:11900:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:11903:0: warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(DST0) = DNWTST
 ^
portsrc.f: In function 'dg7qsb':
portsrc.f:2390:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:2389:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  60   V(DST0) = DS0
 ^
portsrc.f: In function 'dl7msb':
portsrc.f:7892:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:7891:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  90   V(DST0) = DS0
 ^
portsrc.f: In function 'df7hes':
portsrc.f:8370:0: warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
  210  IV(FDH) = HES
 ^
portsrc.f: In function 'dparck':
portsrc.f:3456:0: 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:11737:0: 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:11694:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:11694:0: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f: In function 'drn2g':
portsrc.f:440:0: 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:348:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:348:0: 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-3.3.0/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/datasets'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/datasets'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/methods'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/grid'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
byte-compiling package 'splines'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/splines'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats4'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/stats4'
byte-compiling package 'stats4'
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make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/stats4'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/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    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_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    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_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    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_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-3.3.0/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk/src'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk'
byte-compiling package 'tcltk'
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make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/tcltk'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
make[5]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
make[4]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
byte-compiling package 'parallel'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/parallel'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/base'
installing parsed NAMESPACE files
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
you should 'make docs' now ...
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc'
creating NEWS
creating NEWS.pdf
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/doc/html'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/html'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
installing parsed Rd
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
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make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
building/updating package metadata ...
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
writing package indices
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
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make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
building all R object docs
  converting help for package 'base'
    Arithmetic                              html  
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    AsIs                                    html  
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    Colon                                   html  
    Comparison                              html  
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    Constants                               html  
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    Cstack_info                             html  
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    Dates                                   html  
    Defunct                                 html  
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    Encoding                                html  
    EnvVar                                  html  
    Extract                                 html  
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    Extremes                                html  
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    Hyperbolic                              html  
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    InternalMethods                         html  
    La_version                              html  
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    Log                                     html  
    Logic                                   html  
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    LongVectors                             html  
    MathFun                                 html  
    Memory-limits                           html  
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    NumericConstants                        html  
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    Rhome                                   html  
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    Trig                                    html  
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    aperm                                   html  
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    apply                                   html  
    args                                    html  
    array                                   html  
    as.Date                                 html  
    as.POSIXlt                              html  
Rd warning: /builddir/build/BUILD/R-3.3.0/src/library/base/man/as.POSIXlt.Rd:126: missing file link 'format.POSIXlt'
    as.data.frame                           html  
    as.environment                          html  
    as.function                             html  
    assign                                  html  
    assignOps                               html  
    attach                                  html  
    attr                                    html  
    attributes                              html  
    autoload                                html  
    backsolve                               html  
    base-defunct                            html  
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    base-internal                           html  
    base-package                            html  
    basename                                html  
    bincode                                 html  
    bindenv                                 html  
    bitwise                                 html  
    body                                    html  
    bquote                                  html  
    browser                                 html  
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    builtins                                html  
    by                                      html  
    c                                       html  
    call                                    html  
    callCC                                  html  
    capabilities                            html  
    cat                                     html  
    cbind                                   html  
    char.expand                             html  
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    chartr                                  html  
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    chol                                    html  
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    class                                   html  
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    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  
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    data.class                              html  
    data.frame                              html  
    data.matrix                             html  
    dataframeHelpers                        html  
    date                                    html  
    dcf                                     html  
    debug                                   html  
    delayedAssign                           html  
    deparse                                 html  
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    det                                     html  
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    dev                                     html  
    diag                                    html  
    diff                                    html  
    difftime                                html  
    dim                                     html  
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    do.call                                 html  
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    double                                  html  
    dput                                    html  
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    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  
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    invisible                               html  
    is.finite                               html  
    is.function                             html  
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    is.recursive                            html  
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    isR                                     html  
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    jitter                                  html  
    kappa                                   html  
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    l10n_info                               html  
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    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  
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    match.fun                               html  
    matmult                                 html  
    matrix                                  html  
    maxCol                                  html  
    mean                                    html  
    memCompress                             html  
    memory.profile                          html  
    merge                                   html  
    message                                 html  
    missing                                 html  
    mode                                    html  
    name                                    html  
    names                                   html  
    nargs                                   html  
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    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-3.3.0/src/library/base/man/print.Rd:82: missing file link '.print.via.format'
    print.dataframe                         html  
    print.default                           html  
    prmatrix                                html  
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    prod                                    html  
    prop.table                              html  
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    rapply                                  html  
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    readBin                                 html  
    readChar                                html  
    readLines                               html  
    readRDS                                 html  
    readRenviron                            html  
    readline                                html  
    reg.finalizer                           html  
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    regmatches                              html  
    rep                                     html  
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    rev                                     html  
    rle                                     html  
    rm                                      html  
    round.POSIXt                            html  
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    row.names                               html  
    rowsum                                  html  
    sQuote                                  html  
    sample                                  html  
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    seq.Date                                html  
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    serialize                               html  
    setTimeLimit                            html  
    sets                                    html  
    shQuote                                 html  
    showConnections                         html  
    sign                                    html  
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    slice.index                             html  
    slotOp                                  html  
    socketSelect                            html  
    solve                                   html  
    sort                                    html  
    source                                  html  
    split                                   html  
    sprintf                                 html  
    srcfile                                 html  
    standardGeneric                         html  
    startsWith                              html  
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    strptime                                html  
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    subset                                  html  
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  converting help for package 'tools'
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Rd warning: /builddir/build/BUILD/R-3.3.0/src/library/tools/man/check_packages_in_dir.Rd:113: missing file link 'parLapply'
    codoc                                   html  
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    find_gs_cmd                             html  
    getDepList                              html  
    getVignetteInfo                         html  
    installFoundDepends                     html  
    loadRdMacros                            html  
    makeLazyLoading                         html  
    make_translations_pkg                   html  
    makevars                                html  
    md5sum                                  html  
    package.dependencies                    html  
    package_dependencies                    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  
    update_pkg_po                           html  
    vignetteDepends                         html  
    vignetteEngine                          html  
    writePACKAGES                           html  
    xgettext                                html  
  converting help for package 'utils'
    BATCH                                   html  
    INSTALL                                 html  
    PkgUtils                                html  
    Question                                html  
    REMOVE                                  html  
    RHOME                                   html  
    RShowDoc                                html  
    RSiteSearch                             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  
    aspell-utils                            html  
    aspell                                  html  
    available.packages                      html  
    bibentry                                html  
    browseEnv                               html  
    browseURL                               html  
    browseVignettes                         html  
    bug.report                              html  
    capture.output                          html  
    changedFiles                            html  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citEntry                                html  
    citation                                html  
    cite                                    html  
    close.socket                            html  
    combn                                   html  
    compareVersion                          html  
    contrib.url                             html  
    count.fields                            html  
    create.post                             html  
    data                                    html  
    dataentry                               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  
    glob2rx                                 html  
    globalVariables                         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  
    localeToCharset                         html  
    ls_str                                  html  
    maintainer                              html  
    make.packages.html                      html  
    make.socket                             html  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    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  
    recover                                 html  
    relist                                  html  
    remove.packages                         html  
    removeSource                            html  
    roman                                   html  
    rtags                                   html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         html  
    sourceutils                             html  
    stack                                   html  
    str                                     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  
    write.table                             html  
    zip                                     html  
    COMPILE                                 html  
    LINK                                    html  
    memory.size                             html  
    nsl                                     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  
    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  
    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  
    recordGraphics                          html  
    recordplot                              html  
    rgb                                     html  
    rgb2hsv                                 html  
    trans3d                                 html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    quartz                                  html  
    quartzFonts                             html  
    savePlot                                html  
    x11                                     html  
    x11Fonts                                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  
    Documentation                           html  
    EmptyMethodsList-class                  html  
    EnvironmentClass                        html  
    GenericFunctions                        html  
    LanguageClasses                         html  
    LinearMethodsList-class                 html  
    MethodDefinition-class                  html  
    MethodSupport                           html  
    MethodWithNext-class                    html  
    Methods                                 html  
    MethodsList-class                       html  
    MethodsList                             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  
    representation                          html  
    selectSuperClasses                      html  
    setClass                                html  
    setClassUnion                           html  
    setGeneric                              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  
    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  
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  converting help for package 'splines'
    asVector                                html  
    backSpline                              html  
    bs                                      html  
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    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  
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  converting help for package 'compiler'
    compile                                 html  
  converting help for package 'parallel'
    RngStream                               html  
    clusterApply                            html  
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    makeCluster                             html  
    parallel-package                        html  
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make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/Recommended'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/tmp/RtmpXCqVNu/R.INSTALL1ace394755e4/MASS/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/lib -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpXCqVNu/R.INSTALL1ace394755e4/MASS/src'
installing to /builddir/build/BUILD/R-3.3.0/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  
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    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
** libs
make[3]: Entering directory `/tmp/RtmpPJmXHr/R.INSTALL1afd5a504f0c/lattice/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/lib -Wl,-z,relro -o lattice.so init.o threeDplot.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpPJmXHr/R.INSTALL1afd5a504f0c/lattice/src'
installing to /builddir/build/BUILD/R-3.3.0/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  
    axis.default                            html  
    banking                                 html  
    barchart.table                          html  
    barley                                  html  
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    draw.colorkey                           html  
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    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  
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    panel.densityplot                       html  
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    panel.functions                         html  
    panel.histogram                         html  
    panel.levelplot                         html  
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    panel.parallel                          html  
    panel.qqmath                            html  
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    panel.smoothScatter                     html  
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    prepanel.functions                      html  
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    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
** libs
make[3]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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
Csparse.c: In function 'Csparse_to_dense':
Csparse.c:155:5: warning: "/*" within comment [-Wcomment]
     /* TODO: use cholmod_l_* but also the 'cl' global ==> many changes in chm_common.[ch]
 ^
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD/Source'
make[5]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD/Source'
make[5]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/SuiteSparse_config'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD'
( cd Lib ; make )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD/Lib'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD'
( cd Source ; make lib )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD/Source'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD'
( cd Source ; make lib )
make[5]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD/Source'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD'
make[4]: Entering directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/builddir/build/BUILD/R-3.3.0/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-3.3.0/lib -lRlapack -L/builddir/build/BUILD/R-3.3.0/lib -lRblas -lgfortran -lm -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src'
installing to /builddir/build/BUILD/R-3.3.0/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'image' from package 'graphics' in package 'Matrix'
Creating a generic function for 'solve' from package 'base' in package 'Matrix'
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 'determinant' from package 'base' in package 'Matrix'
Creating a generic function for 'update' from package 'stats' in package 'Matrix'
Creating a generic function for 't' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'as.matrix' from package 'base' in package 'Matrix'
Creating a generic function for 'as.array' from package 'base' in package 'Matrix'
Creating a generic function for 'head' from package 'utils' in package 'Matrix'
Creating a generic function for 'tail' from package 'utils' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'mean' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'isSymmetric' from package 'base' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'chol' 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'
Creating a generic function for 'all.equal' from package 'base' in package 'Matrix'
Creating a generic function for 'diff' 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 'qr' 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 'print' from package 'base' in package 'Matrix'
Creating a generic function for 'summary' 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 'format' from package 'base' in package 'Matrix'
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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/man/abIndex-class.Rd:80: missing file link 'Ops'
    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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/man/image-methods.Rd:53: missing file link 'panel.levelplot.raster'
    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/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/man/matrix-products.Rd:405: missing file link 'tcrossprod'
    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
Loading required package: Matrix
** 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
** libs
make[3]: Entering directory `/tmp/RtmpUCf6aG/R.INSTALL1e3220ae4f24/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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
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-3.3.0/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 rs.o -lgfortran -lm -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpUCf6aG/R.INSTALL1e3220ae4f24/nlme/src'
installing to /builddir/build/BUILD/R-3.3.0/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
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    ACF.gls                                 html  
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    gapply                                  html  
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    getResponseFormula                      html  
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    gls-internal                            html  
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    lme                                     html  
    lme.groupedData                         html  
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    lmeObject                               html  
    lmeStruct                               html  
    logDet                                  html  
    logDet.corStruct                        html  
    logDet.pdMat                            html  
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    logLik.corStruct                        html  
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    logLik.gnls                             html  
    logLik.gnlsStruct                       html  
    logLik.lmList                           html  
    logLik.lme                              html  
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    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  
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    plot.intervals.lmList                   html  
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    plot.nffGroupedData                     html  
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    qqnorm.gls                              html  
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    quinModel                               html  
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    update.modelStruct                      html  
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    varClasses                              html  
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    varConstPower                           html  
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    varFixed                                html  
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    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
** libs
make[3]: Entering directory `/tmp/RtmpazimVu/R.INSTALL1ea31fdb2398/survival/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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:329:20: 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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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
coxexact.c: In function 'coxexact':
coxexact.c:309:27: warning: 'sstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 d0 = coxd0(ndeath, nrisk, score+sstart, dmem0, maxdeath);
                           ^
coxexact.c:151:17: warning: 'nrisk' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (maxdeath*nrisk > temp) temp = maxdeath*nrisk;
                 ^
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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
survfitci.c: In function 'survfitci':
survfitci.c:30:14: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double **umat;     /* per subject leverage at this time point */
              ^
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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 chsolve2.o chsolve3.o concordance1.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 init.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpazimVu/R.INSTALL1ea31fdb2398/survival/src'
installing to /builddir/build/BUILD/R-3.3.0/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  
    aareg                                   html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    dsurvreg                                html  
    finegray                                html  
    flchain                                 html  
    frailty                                 html  
    genfan                                  html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  html  
    lines.survfit                           html  
    logLik.coxph                            html  
    logan                                   html  
    lung                                    html  
    mgus                                    html  
    mgus2                                   html  
    model.frame.coxph                       html  
    model.matrix.coxph                      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  
    residuals.coxph                         html  
    residuals.survreg                       html  
    retinopathy                             html  
    ridge                                   html  
    stanford2                               html  
    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.survexp                         html  
    summary.survfit                         html  
    survConcordance                         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  
    untangle.specials                       html  
    uspop2                                  html  
    veteran                                 html  
** 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
** 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
** libs
make[3]: Entering directory `/tmp/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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 mona.f -o mona.o
Warning: Nonexistent include directory "/usr/lib/gfortran/modules"
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/src'
installing to /builddir/build/BUILD/R-3.3.0/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/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/man/clusplot.default.Rd:209: missing file link 'cov.mve'
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
    diana                                   html  
    dissimilarity.object                    html  
    ellipsoidhull                           html  
Rd warning: /tmp/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/man/ellipsoidhull.Rd:36: missing file link 'cov.mve'
Rd warning: /tmp/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/man/ellipsoidhull.Rd:87: missing file link 'cov.mve'
    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/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/man/plot.agnes.Rd:73: missing file link 'plot.dendrogram'
    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/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/man/print.dissimilarity.Rd:27: missing file link 'print.dist'
    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
** 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
** libs
make[3]: Entering directory `/tmp/Rtmpom9YA1/R.INSTALL1ffd7ceeb4eb/foreign/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmpom9YA1/R.INSTALL1ffd7ceeb4eb/foreign/src'
installing to /builddir/build/BUILD/R-3.3.0/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
** libs
make[3]: Entering directory `/tmp/RtmpR5gvAu/R.INSTALL204254a6e66c/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-3.3.0/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-3.3.0/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-3.3.0/lib -lRblas -lgfortran -lm -lgfortran -lm -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpR5gvAu/R.INSTALL204254a6e66c/KernSmooth/src'
installing to /builddir/build/BUILD/R-3.3.0/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
** libs
make[3]: Entering directory `/tmp/RtmpnVX80A/R.INSTALL2089426aefa5/rpart/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpnVX80A/R.INSTALL2089426aefa5/rpart/src'
installing to /builddir/build/BUILD/R-3.3.0/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                                  html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
** 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
** libs
make[3]: Entering directory `/tmp/RtmpZbQ7a6/R.INSTALL21016ef39a20/class/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/lib -Wl,-z,relro -o class.so class.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpZbQ7a6/R.INSTALL21016ef39a20/class/src'
installing to /builddir/build/BUILD/R-3.3.0/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
** libs
make[3]: Entering directory `/tmp/Rtmpno8E2U/R.INSTALL211b60e350de/nnet/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/lib -Wl,-z,relro -o nnet.so nnet.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmpno8E2U/R.INSTALL211b60e350de/nnet/src'
installing to /builddir/build/BUILD/R-3.3.0/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
** libs
make[3]: Entering directory `/tmp/RtmpuxstG4/R.INSTALL21416c3402d2/spatial/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/lib -Wl,-z,relro -o spatial.so init.o krc.o pps.o -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpuxstG4/R.INSTALL21416c3402d2/spatial/src'
installing to /builddir/build/BUILD/R-3.3.0/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  
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    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
** libs
make[3]: Entering directory `/tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/src'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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 'tensorXty':
discrete.c:101:19: warning: unused variable 'q' [-Wunused-variable]
   int pb=1,i,j,pd,q;
                   ^
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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 'getXXt':
mat.c:1159:9: warning: unused variable 'j' [-Wunused-variable]
   int i,j;
         ^
mat.c:1159:7: warning: unused variable 'i' [-Wunused-variable]
   int i,j;
       ^
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/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-3.3.0/lib -lRlapack -L/builddir/build/BUILD/R-3.3.0/lib -lRblas -lgfortran -lm -fopenmp -L/builddir/build/BUILD/R-3.3.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/src'
installing to /builddir/build/BUILD/R-3.3.0/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  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
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    anova.gam                               html  
    bam                                     html  
Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/bam.Rd:13: missing file link 'parallel'
Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/bam.Rd:136: missing file link 'parLapply'
Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/bam.Rd:191: missing file link 'makeForkCluster'
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    family.mgcv                             html  
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    linear.functional.terms                 html  
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    magic.post.proc                         html  
    mgcv-FAQ                                html  
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    mgcv-parallel                           html  
Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/mgcv-parallel.Rd:11: missing file link 'parallel'
    missing.data                            html  
    model.matrix.gam                        html  
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    pen.edf                                 html  
    place.knots                             html  
    plot.gam                                html  
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    predict.bam                             html  
Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/predict.bam.Rd:76: missing file link 'parLapply'
    predict.gam                             html  
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    rTweedie                                html  
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    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  
    smoothCon                               html  
    sp.vcov                                 html  
    spasm.construct                         html  
    step.gam                                html  
    summary.gam                             html  
    t2                                      html  
    te                                      html  
    tensor.prod.model.matrix                html  
    trichol                                 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-3.3.0/src/library/Recommended'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library/Recommended'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0'
configuring Java ...
Java interpreter : /usr/bin/java
Java version     : 1.8.0_91
Java home path   : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.91-0.b14.el7.arm/jre
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/arm/server -ljvm
make[2]: Entering directory `/tmp/Rjavareconf.2EpnRV'
gcc -std=gnu99 -I/builddir/build/BUILD/R-3.3.0/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.2EpnRV'
make[2]: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME        : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.91-0.b14.el7.arm/jre
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /builddir/build/BUILD/R-3.3.0
Done.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0'
+ cd src/nmath/standalone
+ make
(cd ../../include; make Rmath.h)
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include'
Copying source files
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 expm1.d from expm1.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-3.3.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 expm1.c -o expm1.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 expm1.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-3.3.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/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 expm1.c -o expm1.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 expm1.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
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[]\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]
Underfull \hbox (badness 10000) in paragraph at lines 2079--2081
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2186--2186
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[35] [36]
Underfull \hbox (badness 1107) in paragraph at lines 2319--2321
[]\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
[37] [38] [39] [40] [41]
Underfull \hbox (badness 5878) in paragraph at lines 2650--2655
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
Underfull \hbox (badness 10000) in paragraph at lines 2650--2655
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55]
Underfull \hbox (badness 10000) in paragraph at lines 3580--3582
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[56] [57] [58] [59] [60] [61]
Underfull \hbox (badness 4927) in paragraph at lines 4030--4034
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\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
[62] [63] [64]
Underfull \hbox (badness 4595) in paragraph at lines 4174--4177
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[65] [66]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4329--4329
 []\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 4359--4365
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[67]
Underfull \hbox (badness 10000) in paragraph at lines 4450--4455
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
Underfull \hbox (badness 10000) in paragraph at lines 4450--4455
[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
Underfull \hbox (badness 2181) in paragraph at lines 4450--4455
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[68]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4529--4529
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[69] [70] [71] [72]
Underfull \hbox (badness 2521) in paragraph at lines 4782--4784
[]\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
[73] [74] [75] [76] [77] [78]
Underfull \hbox (badness 10000) in paragraph at lines 5168--5176
[]\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
[79] [80] [81] [82] [83] [84] [85] [86]
Underfull \hbox (badness 1796) in paragraph at lines 5713--5721
[]\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 : / /
[87] [88] [89]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5907--5907
 []\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 5909--5909
 []\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 5910--5910
 []\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}[] 
[90] [91]
Underfull \hbox (badness 1635) in paragraph at lines 6069--6072
[]\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 6073--6076
[]\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
Underfull \hbox (badness 1102) in paragraph at lines 6090--6103
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 6104--6112
[]\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
[92] [93]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6251--6251
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[94]
Overfull \hbox (107.35893pt too wide) in paragraph at lines 6293--6295
[]\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 : 
[95] [96]
Underfull \hbox (badness 10000) in paragraph at lines 6434--6437
[]\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 6434--6437
\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
[97] [98]
Underfull \hbox (badness 1248) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
Underfull \hbox (badness 2080) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
Underfull \hbox (badness 10000) in paragraph at lines 6618--6620
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[99]
Underfull \hbox (badness 1067) in paragraph at lines 6660--6667
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[100] [101]
Underfull \vbox (badness 10000) has occurred while \output is active [102]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6837--6837
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[103] [104] [105] [106]
Underfull \hbox (badness 10000) in paragraph at lines 7168--7170
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[107] [108]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7313--7313
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[109]
Underfull \hbox (badness 4595) in paragraph at lines 7355--7358
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[110] [111] [112]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7551--7551
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[113] [114]
Underfull \hbox (badness 8132) in paragraph at lines 7652--7656
[]\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 7652--7656
\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 7671--7682
[]\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 1062) in paragraph at lines 7671--7682
[][]\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
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7704--7708
[]\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")
[115] [116] [117] [118] [119] [120]
Underfull \hbox (badness 10000) in paragraph at lines 8146--8158
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8146--8158
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[121] [122] [123]
Underfull \hbox (badness 5802) in paragraph at lines 8351--8355
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[124] [125]
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\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
Underfull \hbox (badness 10000) in paragraph at lines 8528--8532
[]\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
[126] [127]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8616--8616
 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8618--8618
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[128] [129]
Underfull \hbox (badness 4254) in paragraph at lines 8779--8783
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[130]
Underfull \hbox (badness 1132) in paragraph at lines 8839--8846
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[131] [132]
Underfull \hbox (badness 1603) in paragraph at lines 8952--8955
[]\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
[133] [134] [135] [136] [137] [138] [139] [140]
Underfull \hbox (badness 1917) in paragraph at lines 9540--9545
[]\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
[141]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9595--9595
 []\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 9596--9596
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[142] [143]
Underfull \hbox (badness 1168) in paragraph at lines 9698--9703
\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
[144] [145]
Underfull \hbox (badness 2828) in paragraph at lines 9836--9840
[][][]$\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 9836--9840
\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 _
[146] [147] [148]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10067--10067
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[149]
Underfull \hbox (badness 1629) in paragraph at lines 10141--10145
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[150] [151]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 10254--10262
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10263--10265
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[152]
Underfull \hbox (badness 3735) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[153] [154]
Underfull \hbox (badness 10000) in paragraph at lines 10490--10493
[]\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
[155] [156] [157] [158] [159] [160] [161] [162] [163]
Underfull \hbox (badness 5288) in paragraph at lines 11156--11158
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11166--11171
[]\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
[164]
Underfull \hbox (badness 10000) in paragraph at lines 11224--11226
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[165] [166]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\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 11341--11345
\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
[167] [168]
Underfull \hbox (badness 10000) in paragraph at lines 11456--11458
[]\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
Underfull \hbox (badness 2790) in paragraph at lines 11499--11501
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[169] [170] [171]
Underfull \hbox (badness 4048) in paragraph at lines 11669--11679
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 11669--11679
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[172] [173] [174]
Underfull \hbox (badness 5460) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[175] [176] [177] [178] [179]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 12280--12280
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[180] [181] [182] [183]
Underfull \hbox (badness 5119) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[184] [185]
Underfull \hbox (badness 2221) in paragraph at lines 12703--12709
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[186] [187] [188]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[189] [190]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[191] [192]
Underfull \hbox (badness 10000) in paragraph at lines 13205--13207
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[193] [194]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\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 (30.78088pt too wide) in paragraph at lines 13355--13355
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[195] [196]
Underfull \hbox (badness 10000) in paragraph at lines 13447--13450
[][][]\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 ,
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 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[197]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
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[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 13569--13576
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 13569--13576
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
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[]\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,
[198] [199] [200]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
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 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[201] [202]
Underfull \hbox (badness 10000) in paragraph at lines 13820--13824
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
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\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[203] [204]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
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 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[205]
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[]\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-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[206]
Underfull \hbox (badness 6944) in paragraph at lines 14149--14152
[][][]\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 ,
[207]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14308--14310
[]\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
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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
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 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
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[]\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
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[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14369--14373
[]\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
[210]
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[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\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,
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\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14441--14449
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[212]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14545--14545
 []\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 ")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [213]
[214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225]
[226]
Underfull \hbox (badness 2418) in paragraph at lines 15479--15483
\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 15486--15489
[]\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 15514--15521
[][][]\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 ,
[227] [228] [229] [230]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[231] [232] [233] [234]
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 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
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 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [235]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16104--16104
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 16110--16114
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16110--16114
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[236] [237] [238] [239]
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 []\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))) 
[240] [241] [242] [243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16703--16703
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[244] [245] [246] [247]
Underfull \hbox (badness 2435) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
Underfull \hbox (badness 1867) in paragraph at lines 17006--17013
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17006--17013
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
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\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
[248]
Underfull \hbox (badness 2285) in paragraph at lines 17021--17023
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17029--17029
 []\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.[] 
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 []    \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 17059--17059
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[249] [250] [251] [252] [253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17520--17522
[]\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
[256]
Underfull \hbox (badness 4217) in paragraph at lines 17604--17613
[][][]\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 17619--17635
[][][]\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 ,
[257] [258] [259] [260] [261] [262]
Underfull \hbox (badness 4699) in paragraph at lines 18033--18036
[]\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 ,
[263] [264]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[265] [266]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[267] [268] [269] [270] [271] [272]
Underfull \hbox (badness 1430) in paragraph at lines 18700--18705
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 18700--18705
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[273]
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[274]
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[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 18821--18828
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 18821--18828
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
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\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 18837--18839
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[275] [276]
Underfull \hbox (badness 1975) in paragraph at lines 18909--18912
[]\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
[277] [278] [279] [280] [281]
Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\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
[283] [284]
Underfull \hbox (badness 10000) in paragraph at lines 19475--19479
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\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
[285]
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[][][]\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 ,
[286] [287]
Underfull \hbox (badness 10000) in paragraph at lines 19692--19696
[]\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
[288]
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[]\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 19747--19752
\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 19747--19752
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 19747--19752
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[289] [290] [291]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19913--19913
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19917--19917
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Underfull \hbox (badness 3343) in paragraph at lines 19973--19977
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[292] [293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20059--20059
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20070--20070
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[294] [295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20180--20180
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (85.38034pt too wide) in paragraph at lines 20183--20183
 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects
 w/ same name in .GlobalEnv[] 
Underfull \hbox (badness 6380) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[296]
Underfull \hbox (badness 10000) in paragraph at lines 20256--20259
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1337) in paragraph at lines 20285--20292
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 2229) in paragraph at lines 20285--20292
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
Underfull \hbox (badness 1043) in paragraph at lines 20285--20292
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
Underfull \hbox (badness 2564) in paragraph at lines 20304--20307
[]\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
[297]
Underfull \hbox (badness 1205) in paragraph at lines 20357--20362
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[298] [299] [300] [301]
Underfull \hbox (badness 2469) in paragraph at lines 20667--20673
[]\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 1939) in paragraph at lines 20667--20673
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 20667--20673
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[302] [303] [304] [305] [306]
Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 1655) in paragraph at lines 21382--21386
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[313] [314] [315] [316]
Underfull \hbox (badness 2277) in paragraph at lines 21628--21631
[]\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.
[317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 10000) in paragraph at lines 22108--22114
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22108--22114
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
[]\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 2951) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22140--22148
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[324] [325]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22217--22217
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[326]
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[327] [328] [329] [330] [331] [332]
Underfull \hbox (badness 10000) in paragraph at lines 22707--22715
\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 ;
[333]
Underfull \hbox (badness 3849) in paragraph at lines 22821--22826
[]\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
[334]
Underfull \hbox (badness 7308) in paragraph at lines 22898--22904
[]\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 5077) in paragraph at lines 22898--22904
\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 10000) in paragraph at lines 22908--22911
[]\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 22908--22911
\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
[335] [336] [337]
Underfull \hbox (badness 10000) in paragraph at lines 23060--23062
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[338] [339] [340] [341] [342] [343] [344] [345] [346]
Underfull \hbox (badness 2197) in paragraph at lines 23722--23726
[]\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 23722--23726
\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
[347]
Underfull \hbox (badness 2846) in paragraph at lines 23736--23740
[]\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 23736--23740
\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
[348]
Underfull \hbox (badness 10000) in paragraph at lines 23826--23832
[]\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 23826--23832
\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 23839--23841
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[349]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 23890--23890
 [] \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:[] 
[350] [351]
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[352] [353]
Underfull \hbox (badness 4120) in paragraph at lines 24152--24159
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[354]
Underfull \hbox (badness 1694) in paragraph at lines 24288--24291
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[355] [356] [357] [358]
Underfull \hbox (badness 1603) in paragraph at lines 24527--24529
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[359]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 24645--24653
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[360]
Underfull \hbox (badness 5475) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[361]
Underfull \hbox (badness 3271) in paragraph at lines 24764--24767
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[362]
Overfull \vbox (2.42159pt too high) has occurred while \output is active
[363]
Underfull \hbox (badness 3138) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[364]
Underfull \hbox (badness 1194) in paragraph at lines 25047--25050
[]\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 25071--25073
[]\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 25083--25087
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25083--25087
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25088--25094
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25109--25120
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25121--25124
[]\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
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
[]\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 25145--25152
[]\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 10000) in paragraph at lines 25145--25152
\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
Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 25145--25152
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[366] [367] [368] [369]
Underfull \vbox (badness 10000) has occurred while \output is active [370]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25478--25478
 []\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 25491--25495
[]\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 25491--25495
\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)]
[371] [372] [373] [374]
Underfull \hbox (badness 4341) in paragraph at lines 25814--25816
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[375]
Underfull \hbox (badness 4518) in paragraph at lines 25850--25856
[][][]\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
Overfull \hbox (42.18039pt too wide) in paragraph at lines 25872--25872
 []\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 25884--25884
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[376] [377] [378] [379] [380] [381] [382]
Underfull \hbox (badness 10000) in paragraph at lines 26306--26310
[]\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,
[383]
Underfull \hbox (badness 1796) in paragraph at lines 26369--26372
[]\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
[384] [385] [386]
Underfull \hbox (badness 10000) in paragraph at lines 26564--26567
[]\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
[387] [388] [389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 1226) in paragraph at lines 27186--27191
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[396]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27231--27231
 []           \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))[] 
[397] [398] [399] [400]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27497--27497
 []\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 27508--27508
 []\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 27514--27514
 []\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 27515--27515
 []\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 27518--27518
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[401]
Underfull \hbox (badness 7415) in paragraph at lines 27593--27597
[]\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
[402]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27614--27614
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[403]
Underfull \hbox (badness 2418) in paragraph at lines 27762--27773
[]\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
[404] [405]
Underfull \hbox (badness 1248) in paragraph at lines 27886--27893
\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 27886--27893
\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 /
[406]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[407] [408]
Underfull \hbox (badness 1337) in paragraph at lines 28092--28095
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[409]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 28140--28140
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 28157--28168
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 28169--28172
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[410] [411]
Underfull \hbox (badness 1117) in paragraph at lines 28264--28270
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 4048) in paragraph at lines 28639--28644
[]\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 28639--28644
\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 28639--28644
\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 ,
[418] [419] [420] [421] [422] [423] [424] [425]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29177--29177
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[426] [427] [428] [429]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 29460--29462
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[430] [431]
Underfull \hbox (badness 7558) in paragraph at lines 29676--29680
[]\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 29686--29688
[]\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
[432]
Underfull \hbox (badness 5417) in paragraph at lines 29691--29694
[][][]\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 29695--29697
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[433] [434] [435] [436] [437] [438]
Underfull \hbox (badness 10000) in paragraph at lines 30105--30109
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[451] [452] [453]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[454]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31206--31206
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[455]
Underfull \hbox (badness 1158) in paragraph at lines 31310--31315
[]\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
[456]
Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 31337--31343
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[457]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 31413--31418
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[458]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31495--31495
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[459] [460] [461]
Underfull \hbox (badness 2809) in paragraph at lines 31759--31765
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 31766--31769
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473]
Underfull \hbox (badness 1735) in paragraph at lines 32578--32584
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[474]
Underfull \hbox (badness 4303) in paragraph at lines 32594--32597
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[475] [476] [477] [478] [479]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 32915--32915
 []         \T1/pcr/m/n/10 method = c("shell", "quick", "radix"), index.return 
= FALSE)[] 
[480] [481] [482]
Underfull \hbox (badness 2512) in paragraph at lines 33187--33189
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[483] [484] [485] [486]
Underfull \vbox (badness 10000) has occurred while \output is active [487]
[488]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33581--33581
 []\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)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33596--33596
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[489] [490] [491] [492] [493] [494]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34031--34031
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34032--34032
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[495] [496] [497]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 34238--34238
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[498]
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 34322--34332
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[499]
Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 1728) in paragraph at lines 34379--34386
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 34379--34386
\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 34379--34386
\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
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[504] [505] [506]
Underfull \hbox (badness 1163) in paragraph at lines 34851--34858
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 34851--34858
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[507] [508] [509] [510]
Underfull \hbox (badness 1142) in paragraph at lines 35123--35129
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 35138--35138
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[511] [512] [513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35384--35384
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[514]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35428--35428
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[515] [516] [517] [518] [519] [520] [521]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 35860--35860
 []\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 35863--35863
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[522]
Underfull \hbox (badness 10000) in paragraph at lines 35908--35911
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35955--35955
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[523] [524] [525] [526]
Underfull \hbox (badness 2762) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[527]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 36252--36252
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[528] [529]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36417--36417
 []\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. 
[530]
Underfull \hbox (badness 3219) in paragraph at lines 36500--36505
[]\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 36500--36505
\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
[531] [532]
Underfull \hbox (badness 2452) in paragraph at lines 36590--36593
\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 36590--36593
\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
[533] [534]
Underfull \hbox (badness 10000) in paragraph at lines 36777--36781
[]\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
[535]
Underfull \hbox (badness 1584) in paragraph at lines 36792--36795
[]\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
[536] [537] [538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36985--36985
 []\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 
[539] [540]
Underfull \hbox (badness 1082) in paragraph at lines 37120--37123
[]\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
[541] [542] [543]
Underfull \hbox (badness 1038) in paragraph at lines 37308--37311
[]\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
[544] [545] [546] [547] [548]
Underfull \hbox (badness 1515) in paragraph at lines 37647--37650
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[549] [550]
Underfull \hbox (badness 1924) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[551]
Underfull \hbox (badness 4096) in paragraph at lines 37869--37872
[]\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 ,
[552] [553] [554]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38103--38103
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
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 []            \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),[] 
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 []                 \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)))))[] 
[555]
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[]\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
[556]
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[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[557] [558]
Underfull \hbox (badness 1867) in paragraph at lines 38318--38322
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
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[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[559] [560] [561] [562] [563]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val
id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z
one col-
Underfull \hbox (badness 1648) in paragraph at lines 38726--38730
\T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see []
[]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _
[564]
Underfull \hbox (badness 5637) in paragraph at lines 38799--38808
[]\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 Ol-son/IANA
Underfull \hbox (badness 1629) in paragraph at lines 38799--38808
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
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[]\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-
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\T1/ptm/m/n/10 fault on OS X and Win-dows: rec-om-mended on So-laris), the data
base at
Underfull \hbox (badness 1303) in paragraph at lines 38809--38816
\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 '
[565]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / www . twinsun .
[566] [567] [568]
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[]\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
[569] [570]
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 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
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 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[571] [572] [573] [574] [575]
Underfull \hbox (badness 6542) in paragraph at lines 39547--39549
[]\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
[576] [577]
Underfull \hbox (badness 1708) in paragraph at lines 39706--39714
[]\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 39706--39714
\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 10000) in paragraph at lines 39715--39719
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 39715--39719
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
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\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
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[][][]\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;
[578] [579]
Underfull \hbox (badness 3895) in paragraph at lines 39791--39803
[]\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 39791--39803
\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 ,
[580] [581]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[582] [583]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 40117--40117
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 1803) in paragraph at lines 40650--40653
[]\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 ),
Underfull \hbox (badness 2334) in paragraph at lines 40654--40661
[]\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
Underfull \hbox (badness 4726) in paragraph at lines 40680--40684
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 40680--40684
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[592] [593] [594]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[595] [596] [597] [598]
Underfull \hbox (badness 6220) in paragraph at lines 41143--41148
[]\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 41143--41148
\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,
Underfull \hbox (badness 1533) in paragraph at lines 41143--41148
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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[]\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
[599]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[600]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
Underfull \hbox (badness 10000) in paragraph at lines 41243--41246
\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
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[]\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
[601]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[602] [603] [604] [605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[607]
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[]\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
[608]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
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[]\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
[609]) (./compiler-pkg.tex [610]
Chapter 2.
[611] [612] [613]) (./datasets-pkg.tex [614]
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[615] [616] [617] [618] [619]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[620]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[621] [622] [623] [624] [625]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[626] [627]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[628] [629] [630] [631]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[632] [633] [634] [635] [636]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1440--1440
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[637] [638]
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[]\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 1525--1528
\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
[639]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[640] [641]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[642]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[643] [644]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1931--1931
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1932--1932
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[645] [646] [647] [648]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[649] [650] [651] [652] [653] [654] [655] [656]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2674--2677
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[657]
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[658]
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[660]
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[661] [662]
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[663]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[664] [665] [666] [667] [668] [669] [670]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3548--3548
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[671] [672]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[673]
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[674]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[675]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[676] [677] [678] [679] [680] [681] [682] [683] [684] [685]
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[687] [688]) (./grDevices-pkg.tex
Chapter 4.
[689] [690] [691] [692] [693] [694]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[695]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[696] [697] [698] [699] [700] [701] [702] [703] [704]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[705]
Underfull \hbox (badness 1325) in paragraph at lines 1133--1139
\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[706]
Underfull \hbox (badness 10000) in paragraph at lines 1174--1176
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[707]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1226--1226
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[708]
Underfull \hbox (badness 1173) in paragraph at lines 1268--1271
[]\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
[709] [710] [711]
Underfull \hbox (badness 10000) in paragraph at lines 1483--1487
[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
Underfull \hbox (badness 10000) in paragraph at lines 1483--1487
\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
Underfull \hbox (badness 10000) in paragraph at lines 1483--1487
\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 2221) in paragraph at lines 1528--1531
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[712]
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[713] [714] [715]
Underfull \hbox (badness 1565) in paragraph at lines 1756--1761
[]\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 1756--1761
\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
[716]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1839--1839
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[717]
Underfull \hbox (badness 1184) in paragraph at lines 1880--1890
[]\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 1880--1890
\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 ,
[718]
Underfull \hbox (badness 10000) in paragraph at lines 1985--1987
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[719] [720]
Underfull \hbox (badness 6758) in paragraph at lines 2146--2149
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[721] [722]
Underfull \hbox (badness 2326) in paragraph at lines 2253--2263
\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 2253--2263
\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 2253--2263
\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 2253--2263
\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
[723]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2337--2337
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[724] [725] [726] [727] [728] [729]
Underfull \hbox (badness 10000) in paragraph at lines 2712--2713
[730] [731] [732] [733] [734] [735]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3118--3118
 []\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 3119--3119
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
Underfull \hbox (badness 1210) in paragraph at lines 3150--3152
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[736] [737] [738] [739]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3363--3363
 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[740]
Underfull \hbox (badness 3525) in paragraph at lines 3470--3473
[]\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
[741]
Underfull \hbox (badness 1968) in paragraph at lines 3484--3486
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[742] [743] [744] [745]
Underfull \hbox (badness 5939) in paragraph at lines 3778--3783
[]\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 ,
[746] [747] [748] [749] [750]
Underfull \hbox (badness 7576) in paragraph at lines 4151--4158
\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 3701) in paragraph at lines 4151--4158
\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[751] [752]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4268--4268
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[753]
Underfull \hbox (badness 1502) in paragraph at lines 4315--4320
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[754] [755]
Underfull \hbox (badness 4765) in paragraph at lines 4475--4477
[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4489--4489
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[756]
Underfull \hbox (badness 5077) in paragraph at lines 4529--4535
[]\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
Underfull \hbox (badness 1342) in paragraph at lines 4545--4547
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[757]
Underfull \hbox (badness 1874) in paragraph at lines 4622--4630
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[758]
Underfull \hbox (badness 1755) in paragraph at lines 4689--4691
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[759] [760]
Underfull \hbox (badness 7344) in paragraph at lines 4860--4862
[]\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 4871--4875
[][][]\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
[761] [762]
Underfull \hbox (badness 1552) in paragraph at lines 4984--4993
\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 4984--4993
\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 4984--4993
\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 ),
[763]
Underfull \hbox (badness 4686) in paragraph at lines 5027--5033
\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
Underfull \hbox (badness 10000) in paragraph at lines 5053--5060
[]\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 /
[764] [765]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5154--5154
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[766]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5266--5266
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
Underfull \hbox (badness 1648) in paragraph at lines 5272--5276
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 5352--5354
[]\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
Underfull \hbox (badness 1072) in paragraph at lines 5388--5394
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[769] [770] [771] [772] [773]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5711--5711
 []\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 5724--5727
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[774] [775] [776] [777] [778] [779]
Underfull \hbox (badness 1189) in paragraph at lines 6121--6123
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[780] [781]
Underfull \hbox (badness 10000) in paragraph at lines 6219--6221
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
Underfull \hbox (badness 10000) in paragraph at lines 6258--6265
[]\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 1584) in paragraph at lines 6258--6265
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[782]
Underfull \hbox (badness 3088) in paragraph at lines 6342--6346
[]\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
[783]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6387--6387
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
Underfull \hbox (badness 10000) in paragraph at lines 6419--6422
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[784] [785]
Underfull \hbox (badness 5637) in paragraph at lines 6510--6516
\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 ,
Underfull \hbox (badness 1721) in paragraph at lines 6543--6546
[]\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 /
[786] [787] [788]
Underfull \hbox (badness 6157) in paragraph at lines 6695--6698
\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
Underfull \hbox (badness 1231) in paragraph at lines 6706--6708
[]\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
[789] [790] [791]) (./graphics-pkg.tex [792]
Chapter 5.
Underfull \hbox (badness 10000) 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
[793] [794] [795] [796]
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\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-
[797] [798] [799]
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\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
[800] [801] [802]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\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 655--659
[][]\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
Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[804] [805]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[806] [807] [808] [809] [810] [811] [812]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1274--1274
 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\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
[813]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
Underfull \hbox (badness 6893) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
Underfull \hbox (badness 3375) in paragraph at lines 1353--1355
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[814]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1423--1423
 []\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 1424--1424
 []\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 1430--1430
 []\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 1431--1431
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[815] [816] [817] [818] [819]
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[][][]\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
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
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, ylab = "")[] 
[821]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[824] [825] [826] [827] [828]
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\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
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
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[][][]\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
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
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[]\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
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
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par("fg"),[] 
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ex = 0.8, adj = 0)[] 
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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[848]
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ol = "blue")[] 
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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[850]
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[][][]\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
[851] [852]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[853] [854] [855]
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[]\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
[856] [857] [858] [859]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[860]
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\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
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[]\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
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= panel.cor)[] 
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[862]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[863]
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\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 ,
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[]\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.
[866]
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</builddir/build/BUILD/R-3.3.0/library/graphics/help/figures/mai.pdf, id=15088,
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<use /builddir/build/BUILD/R-3.3.0/library/graphics/help/figures/mai.pdf>
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<use /builddir/build/BUILD/R-3.3.0/library/graphics/help/figures/oma.pdf>
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[869 </builddir/build/BUILD/R-3.3.0/library/graphics/help/figures/oma.pdf>]
[870]
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[]\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
[871]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[872]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[873]
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[874] [875] [876]
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yramid" = 5),[] 
[877]
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 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
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[]\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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[878] [879] [880] [881]
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axis = "red")[] 
[882] [883] [884]
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 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[885] [886] [887] [888] [889] [890]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[891] [892]
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[]\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
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[][] 
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[894]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[896]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[897]
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[]\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
[898] [899] [900]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[901]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[902] [903] [904] [905] [906] [907]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[908]
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, add = TRUE),[] 
[909] [910] [911] [912] [913]
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us  =  FALSE,[] 
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us  =  FALSE,[] 
[914]
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[915] [916]
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[917] [918]
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[]\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
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lambda = 2),[] 
[921] [922]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[923] [924]
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 []     \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�...")[] 
[925]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\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
[926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8735 \HeaderA{units}{Graphical Units}{units}
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[928] [929]
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 []\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)[] 
[930]) (./grid-pkg.tex
Chapter 6.
[931] [932] [933] [934] [935] [936]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\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
[937] [938] [939] [940] [941] [942] [943] [944] [945] [946]
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), name="B"),[] 
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), name="C"),[] 
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), name="D")),[] 
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[]\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-
[948] [949] [950]
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[]\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
[951] [952] [953] [954] [955] [956] [957]
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[958] [959] [960]
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ck"), name="r1")[] 
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), name="r2")[] 
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te"), name="r3")[] 
[961]
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[]\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 ,
[962]
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[]\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 2012--2015
[]\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
[963] [964] [965]
Underfull \hbox (badness 2894) in paragraph at lines 2219--2226
[]\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
[966] [967] [968]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2375--2375
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
Underfull \hbox (badness 1430) in paragraph at lines 2387--2392
[]\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-
[969] [970] [971]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2580--2580
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[972] [973] [974] [975]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[976] [977] [978] [979] [980]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3162--3162
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[981]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[982]
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[]\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
[983]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3384--3384
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[984]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3391--3391
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[985] [986] [987]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[988] [989] [990] [991] [992] [993] [994] [995] [996]
Underfull \hbox (badness 1430) in paragraph at lines 4157--4162
[]\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-
[997] [998] [999]
Underfull \hbox (badness 1067) in paragraph at lines 4340--4343
[]\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
[1000]
Underfull \hbox (badness 1430) in paragraph at lines 4386--4391
[]\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-
[1001] [1002] [1003]
Underfull \hbox (badness 7256) in paragraph at lines 4583--4585
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012]
Underfull \hbox (badness 10000) in paragraph at lines 5172--5174
[]\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
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
Underfull \hbox (badness 3449) in paragraph at lines 5860--5866
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 5860--5866
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1024] [1025] [1026] [1027] [1028]
Underfull \hbox (badness 1867) in paragraph at lines 6165--6167
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 6202--6208
[][][]\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 ,
[1029] [1030]
Underfull \hbox (badness 7649) in paragraph at lines 6334--6337
[]\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
[1031] [1032] [1033] [1034]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1035]) (./methods-pkg.tex [1036]
Chapter 7.
[1037] [1038] [1039]
Underfull \hbox (badness 10000) in paragraph at lines 278--285
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
Underfull \hbox (badness 7704) in paragraph at lines 278--285
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
Underfull \hbox (badness 10000) in paragraph at lines 278--285
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 278--285
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1040] [1041] [1042] [1043] [1044] [1045]
Underfull \hbox (badness 1281) in paragraph at lines 658--667
[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1046] [1047]
Underfull \hbox (badness 1546) in paragraph at lines 851--857
[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
Underfull \hbox (badness 3780) in paragraph at lines 851--857
\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 851--857
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058]
[1059] [1060]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1863--1863
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
Underfull \hbox (badness 10000) in paragraph at lines 1907--1909
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1061] [1062]
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[]\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
[1063] [1064] [1065]
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("removeClass.msg", defaul
t=TRUE))[] 
[1066] [1067]
Underfull \hbox (badness 10000) in paragraph at lines 2409--2413
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1068] [1069] [1070]
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[]\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
[1071]
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[]\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
[1072]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1073] [1074]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1075]
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
[1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083]
Underfull \hbox (badness 10000) in paragraph at lines 3562--3566
[]\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
[1084]
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[]\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
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[]
[1085]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1086]
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\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1087] [1088] [1089]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1090] [1091] [1092]
Underfull \hbox (badness 10000) in paragraph at lines 4282--4284
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1093] [1094]
Underfull \hbox (badness 1629) in paragraph at lines 4384--4393
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1095]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1096] [1097] [1098] [1099] [1100] [1101]
Underfull \hbox (badness 10000) in paragraph at lines 4975--4984
[]\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
[1102] [1103] [1104]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
[1106]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1107]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1108] [1109] [1110] [1111]
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[]\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
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5662--5666
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1112] [1113]
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1114] [1115]
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[]\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
[1116] [1117] [1118]
Underfull \hbox (badness 1248) in paragraph at lines 6237--6241
[]\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 6237--6241
\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
[1119] [1120]
Underfull \hbox (badness 4647) in paragraph at lines 6392--6394
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1121] [1122] [1123]
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[1125]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6828 \aliasA{S4}{S3Part}{S4}
                               [1126] [1127] [1128]
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 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 
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 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
[1129]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7096 \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.7098 \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.7099 \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.7101 \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.7102 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\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
[1130]
Underfull \hbox (badness 6708) in paragraph at lines 7176--7188
[]\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 ,
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\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 ,
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\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 ,
[1131] [1132]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\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
[1133] [1134] [1135] [1136] [1137] [1138]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1139] [1140]
Underfull \hbox (badness 2277) in paragraph at lines 7950--7958
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing
[1141]
Underfull \hbox (badness 3128) in paragraph at lines 7995--8000
[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
Underfull \hbox (badness 1052) in paragraph at lines 8032--8039
[]\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
[1142] [1143] [1144] [1145] [1146]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8352--8352
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
Underfull \hbox (badness 1755) in paragraph at lines 8388--8391
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1147] [1148]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8531--8531
 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1149] [1150] [1151] [1152] [1153]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8937--8937
 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8950--8950
 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1154]
[1155]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9048--9048
 []\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 9059--9059
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1156] [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164]
Underfull \hbox (badness 10000) in paragraph at lines 9757--9759
[]\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 9765--9769
[]\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 9765--9769
\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
[1165] [1166] [1167] [1168]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\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
[1169]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\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
[1170] [1171]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\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
[1172]
Underfull \hbox (badness 10000) in paragraph at lines 285--288
[]\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa
s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but
Underfull \hbox (badness 10000) in paragraph at lines 303--311
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1173] [1174]
Underfull \hbox (badness 10000) in paragraph at lines 421--423
[]\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
[1175] [1176] [1177] [1178]
Underfull \hbox (badness 1917) in paragraph at lines 710--719
[]\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 710--719
\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
[1179] [1180]
Underfull \hbox (badness 10000) in paragraph at lines 847--850
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1181] [1182] [1183]
Underfull \hbox (badness 5388) in paragraph at lines 1036--1041
[]\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
[1184]
Underfull \hbox (badness 10000) in paragraph at lines 1060--1068
[]\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 1096--1096
 []\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)[] 
[1185] [1186]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1211--1211
 []                 \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 1225--1225
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1254--1257
[]\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
[1187]
Underfull \hbox (badness 3375) in paragraph at lines 1300--1302
[]\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
[1188] [1189]) (./splines-pkg.tex [1190]
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
[1191] [1192] [1193] [1194] [1195] [1196] [1197]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1198] [1199] [1200] [1201]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 699--699
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1202] [1203] [1204]) (./stats-pkg.tex
Chapter 10.
[1205]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1206] [1207] [1208] [1209] [1210]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1024) in paragraph at lines 846--848
[]\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
[1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225]
Underfull \hbox (badness 10000) in paragraph at lines 1390--1392
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1226]
Underfull \hbox (badness 10000) in paragraph at lines 1506--1510
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1506--1510
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1506--1510
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
Underfull \hbox (badness 10000) in paragraph at lines 2079--2084
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2079--2084
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2079--2084
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2085--2091
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2085--2091
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1236]
Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1237] [1238] [1239] [1240]
Underfull \hbox (badness 1221) in paragraph at lines 2431--2436
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2431--2436
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1241]
Underfull \hbox (badness 3965) in paragraph at lines 2508--2510
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1242] [1243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2643--2643
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1244] [1245] [1246] [1247]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2883--2883
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1248] [1249] [1250]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3076--3078
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1251]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3123--3123
 []\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 3124--3124
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1252] [1253] [1254] [1255] [1256]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3502--3502
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1257] [1258] [1259] [1260]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3772--3772
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1261] [1262] [1263] [1264] [1265]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4057--4057
 []\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 4058--4058
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1266] [1267] [1268] [1269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4293--4293
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1270] [1271]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4461--4461
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1272] [1273]
Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
[1274] [1275] [1276] [1277] [1278]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4913--4913
 []\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 4915--4915
 []\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))[] 
[1279]
Underfull \hbox (badness 7397) in paragraph at lines 5002--5006
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5002--5006
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1280] [1281]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5136--5136
 []\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 5154--5154
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1282]
Underfull \hbox (badness 2680) in paragraph at lines 5181--5183
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5186--5188
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1283] [1284] [1285]
Underfull \hbox (badness 1436) in paragraph at lines 5364--5369
[]\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 5364--5369
\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 5364--5369
\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 ,
[1286] [1287]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5550--5550
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1288]
Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1289] [1290]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5716--5716
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1291] [1292] [1293]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5901--5901
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1294] [1295] [1296]
Underfull \hbox (badness 10000) in paragraph at lines 6064--6069
[]\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
[1297] [1298] [1299]
Underfull \hbox (badness 5954) in paragraph at lines 6260--6262
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1300]
Underfull \hbox (badness 2503) in paragraph at lines 6342--6345
[]\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 6346--6348
[]\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 6349--6354
\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 6384--6387
[][][]\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
[1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6419--6419
 []\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 6434--6434
 []\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):[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1302]
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 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1303] [1304] [1305]
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 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1306] [1307] [1308] [1309] [1310] [1311]
Underfull \hbox (badness 10000) in paragraph at lines 7062--7066
\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
[1312]
Underfull \hbox (badness 6493) in paragraph at lines 7159--7162
[]\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
[1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320]
Underfull \hbox (badness 10000) in paragraph at lines 7706--7711
[]\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 , ...,
[1321] [1322]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7844--7846
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1323] [1324] [1325]
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[]\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
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 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8527--8527
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8530--8530
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1333] [1334]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8668--8668
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1335]
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1336] [1337] [1338] [1339] [1340]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9060--9060
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1341] [1342]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1343] [1344] [1345] [1346] [1347] [1348] [1349]
Underfull \hbox (badness 2443) in paragraph at lines 9680--9686
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1350] [1351] [1352]
Underfull \hbox (badness 3758) in paragraph at lines 9894--9897
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1353] [1354] [1355] [1356]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1357]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1358]
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[]\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
[1359] [1360] [1361]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1362]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1363]
Underfull \hbox (badness 10000) in paragraph at lines 10620--10626
[][][]\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,
Underfull \hbox (badness 1418) in paragraph at lines 10658--10663
\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 (=
[1364] [1365]
Underfull \hbox (badness 2635) in paragraph at lines 10791--10794
\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
[1366] [1367] [1368]
Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
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[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
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\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1369]
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 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1370]
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 []            \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 11121--11125
[]\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
[1371] [1372] [1373]
Underfull \hbox (badness 7379) in paragraph at lines 11300--11303
[]\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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1374] [1375]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11439--11439
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1376]
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 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11518--11518
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1377]
Underfull \hbox (badness 1062) in paragraph at lines 11566--11571
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1378] [1379]
Underfull \hbox (badness 3623) in paragraph at lines 11711--11713
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1380]
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 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1381] [1382]
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 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1383]
Underfull \hbox (badness 10000) in paragraph at lines 11940--11943
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1384] [1385] [1386]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
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[]\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
[1387]
Underfull \hbox (badness 2753) in paragraph at lines 12232--12234
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1388] [1389]
Underfull \hbox (badness 1292) in paragraph at lines 12357--12361
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1390] [1391]
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\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 12476--12480
\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
[1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1402] [1403] [1404]
Underfull \hbox (badness 10000) in paragraph at lines 13365--13369
[]\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
 ,
[1405] [1406] [1407]
Underfull \hbox (badness 6995) in paragraph at lines 13550--13552
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1408] [1409]
Underfull \hbox (badness 1163) in paragraph at lines 13698--13706
\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 ,
[1410] [1411]
Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1412] [1413]
Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 13956--13960
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1414]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14004--14004
 []\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 14005--14005
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1415]
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[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14060--14063
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1416] [1417] [1418] [1419]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14346--14346
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
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 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1420]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14397--14399
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14440--14440
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1421] [1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 2726) in paragraph at lines 14843--14846
[]\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 ,
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15555--15555
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1439] [1440]
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[]\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,
[1441]
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\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
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\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
[1442]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15824--15824
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16377--16377
 []\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[] 
[1451] [1452] [1453]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16605--16605
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1454] [1455] [1456] [1457] [1458] [1459] [1460]
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[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
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\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1461] [1462]
Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1463]
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 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1466]
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[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1467]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17490--17490
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1468]
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 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17584--17584
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476]
Underfull \hbox (badness 1248) in paragraph at lines 18074--18077
[]\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 1127) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1477]
Underfull \hbox (badness 1478) in paragraph at lines 18095--18099
\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
Underfull \hbox (badness 2042) in paragraph at lines 18148--18150
[]\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
[1478] [1479]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18244--18244
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1480]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18286--18286
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18319--18319
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1481]
Underfull \hbox (badness 2564) in paragraph at lines 18357--18368
[]\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 18357--18368
\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
[1482]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18420--18420
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1483] [1484] [1485]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18635--18635
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1486]
Underfull \hbox (badness 1337) in paragraph at lines 18711--18714
[]\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
[1487] [1488] [1489] [1490] [1491]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19027--19027
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1492] [1493]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19115--19115
 []       \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 (6.78088pt too wide) in paragraph at lines 19118--19118
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1494] [1495] [1496] [1497] [1498]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19434--19434
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 4779) in paragraph at lines 19441--19443
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1499]
Underfull \hbox (badness 1107) in paragraph at lines 19502--19504
[]\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
[1500]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19557--19557
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19564--19564
 []\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)[] 
[1501]
Underfull \hbox (badness 10000) in paragraph at lines 19614--19617
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 19614--19617
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1502]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19658--19658
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1503] [1504]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19780--19780
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1505]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19886--19886
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1506]
Underfull \hbox (badness 10000) in paragraph at lines 19941--19943
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1507]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19978--19978
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
[1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518]
[1519] [1520]
Underfull \hbox (badness 6859) in paragraph at lines 20852--20859
[][][]\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 20863--20869
[]\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 ,
[1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]
[1532] [1533] [1534] [1535] [1536] [1537]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21875--21875
 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1538] [1539] [1540] [1541] [1542]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
[1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552]
Underfull \hbox (badness 1028) in paragraph at lines 22881--22884
[]\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
[1553] [1554]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22991--22994
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1555] [1556] [1557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23202--23202
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1558] [1559] [1560]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23422--23422
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1561] [1562]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\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
[1563]
Underfull \hbox (badness 2134) in paragraph at lines 23619--23623
[][][]\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 23632--23632
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1564] [1565] [1566] [1567] [1568] [1569] [1570]
Underfull \hbox (badness 2591) in paragraph at lines 24089--24095
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1571] [1572] [1573]
Underfull \hbox (badness 1867) in paragraph at lines 24286--24288
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1574]
Underfull \hbox (badness 10000) in paragraph at lines 24299--24301
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24333--24333
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1575] [1576] [1577]
Underfull \hbox (badness 2495) in paragraph at lines 24523--24532
[]\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 .
[1578]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24605--24605
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1579]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24699--24699
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1580]
Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 24757--24762
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1581] [1582]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24916--24916
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1583] [1584] [1585]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25086--25086
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1586]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25153--25153
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1587] [1588] [1589] [1590] [1591] [1592]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25529--25529
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
Underfull \hbox (badness 6477) in paragraph at lines 25582--25585
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1593] [1594]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25708--25708
 []\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 25709--25709
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1595]
Underfull \hbox (badness 2922) in paragraph at lines 25775--25780
[]\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
[1596]
Underfull \hbox (badness 2922) in paragraph at lines 25837--25842
[]\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
Underfull \hbox (badness 3240) in paragraph at lines 25849--25853
[][][]\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
[1597]
Underfull \hbox (badness 2922) in paragraph at lines 25894--25899
[]\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
[1598]
Underfull \hbox (badness 2922) in paragraph at lines 25955--25961
[]\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
[1599]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25977--25977
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25993--25993
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1600] [1601]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26107--26107
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26130--26130
 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1602]
Underfull \hbox (badness 2922) in paragraph at lines 26168--26173
[]\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
[1603]
Underfull \hbox (badness 2922) in paragraph at lines 26224--26229
[]\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
Underfull \hbox (badness 2922) in paragraph at lines 26281--26286
[]\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
[1604]
Underfull \hbox (badness 2922) in paragraph at lines 26336--26341
[]\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
[1605]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26357--26357
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
Underfull \hbox (badness 6493) in paragraph at lines 26405--26410
[]\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
[1606]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26431--26431
 []\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 26433--26433
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1607] [1608] [1609] [1610] [1611] [1612] [1613]
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1614] [1615] [1616] [1617] [1618] [1619] [1620]
Underfull \hbox (badness 3396) in paragraph at lines 27358--27360
[]\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
[1621] [1622] [1623]
Underfull \hbox (badness 2237) in paragraph at lines 27535--27537
[]\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
[1624] [1625]
Underfull \hbox (badness 2591) in paragraph at lines 27699--27701
[]\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
[1626]
Underfull \hbox (badness 2237) in paragraph at lines 27745--27748
[]\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
[1627] [1628] [1629]
Underfull \hbox (badness 3407) in paragraph at lines 27924--27928
[]\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)
[1630] [1631]
Underfull \hbox (badness 1337) in paragraph at lines 28057--28061
[]\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
[1632] [1633]
Underfull \hbox (badness 10000) in paragraph at lines 28174--28177
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
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main = t.tit,[] 
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mon",[] 
[1636]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1637]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1638]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
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[]\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
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1649]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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v = FALSE,[] 
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 []\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:[] 
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[]\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
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
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ALSE, 
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ALSE)[] 
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[]\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
[1674] [1675]
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1676]) (./stats4-pkg.tex
Chapter 11.
[1677] [1678] [1679]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1680] [1681] [1682]pdfTeX warning (ext4): destination with the same identifier
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1684] [1685]) (./tcltk-pkg.tex [1686]
Chapter 12.
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1706]) (./tools-pkg.tex
Chapter 13.
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer /
 en / opentype /
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xz"),[] 
[1721]
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mpress == "none")[] 
[1722]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
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n-den-cies (de-
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
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pre-vi-ous
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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tm/m/n/10 and
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r-it-ing from class
[1726]
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[]\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
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
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hances"))[] 
[1730]
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs
t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age
[1740]
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ogo.svg}{options: width=100}",[] 
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dth=0.5in}}}"),[] 
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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
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0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
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\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
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\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
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
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Rd"),[] 
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[]\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
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[]\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
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[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
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,
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[]\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
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bugs) 
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\T1/ptm/m/n/10 ' and
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[]\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
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
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he
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\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
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
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pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1769] [1770] [1771]
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\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 ,
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
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[1772]
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[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1773] [1774]) (./utils-pkg.tex
Chapter 14.
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[]\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 ',
[1775] [1776] [1777]
Underfull \hbox (badness 1038) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1778]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1779] [1780] [1781]
Underfull \hbox (badness 1888) in paragraph at lines 450--454
[]\T1/ptm/m/n/10 Kurt Hornik and Dun-can Mur-doch (2011), Watch your spelling! 
\T1/ptm/m/it/10 The R Jour-nal \T1/ptm/b/n/10 3\T1/ptm/m/n/10 (2),
Overfull \hbox (0.78088pt too wide) in paragraph at lines 500--500
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1782]
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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Underfull \hbox (badness 10000) in paragraph at lines 543--549
[]\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 543--549
\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-
[1783] [1784]
Underfull \hbox (badness 4505) in paragraph at lines 657--663
\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
[1785]
Underfull \hbox (badness 1603) in paragraph at lines 774--780
\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
Underfull \hbox (badness 3029) in paragraph at lines 774--780
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1786]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 827--827
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1787] [1788]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1789]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1044--1044
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1790] [1791] [1792] [1793] [1794] [1795]
Underfull \hbox (badness 1859) in paragraph at lines 1402--1411
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1796]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1503--1503
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1797]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1538--1538
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1798] [1799]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1684--1684
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1704--1704
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1800]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
Underfull \hbox (badness 2213) in paragraph at lines 1801--1804
[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1801] [1802]
Underfull \hbox (badness 10000) in paragraph at lines 1901--1903
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1803]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
Underfull \hbox (badness 5189) in paragraph at lines 1991--1993
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1804]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1805]
Underfull \hbox (badness 1082) in paragraph at lines 2140--2144
[][][]\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;
[1806]
Underfull \hbox (badness 10000) in paragraph at lines 2177--2179
[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2209--2216
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1807]
Underfull \hbox (badness 10000) in paragraph at lines 2221--2223
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1808] [1809] [1810]
Underfull \hbox (badness 10000) in paragraph at lines 2399--2401
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1811] [1812] [1813]
Underfull \hbox (badness 10000) in paragraph at lines 2635--2639
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
Underfull \hbox (badness 5203) in paragraph at lines 2635--2639
[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
Overfull \hbox (133.10922pt too wide) in paragraph at lines 2640--2643
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 2689--2692
[]\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
[1815]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2761--2761
 []\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 '[] 
[1816]
Underfull \hbox (badness 2452) in paragraph at lines 2837--2840
[]\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
[1817] [1818] [1819] [1820] [1821] [1822]
Underfull \hbox (badness 1072) in paragraph at lines 3246--3254
[]\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
Underfull \hbox (badness 1231) in paragraph at lines 3289--3295
[]\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 3296--3301
[]\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 3296--3301
\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 3296--3301
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1823] [1824]
Underfull \hbox (badness 4660) in paragraph at lines 3401--3404
\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
[1825] [1826] [1827]
Underfull \hbox (badness 1565) in paragraph at lines 3607--3611
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3628--3634
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1828]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3690--3690
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
Overfull \hbox (2.55087pt too wide) in paragraph at lines 3718--3725
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1829] [1830] [1831] [1832] [1833]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4038--4038
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1834]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4109 ...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.4109 ...mat Unordered and Ordered Lists}{format}
                                                   [1835] [1836] [1837]
[1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848]
[1849]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5018--5018
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1850]
Underfull \hbox (badness 10000) in paragraph at lines 5102--5104
[]\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
[1851]
Underfull \hbox (badness 1502) in paragraph at lines 5151--5156
[]\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 5151--5156
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1852] [1853]
Underfull \hbox (badness 10000) in paragraph at lines 5324--5333
[]\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 5324--5333
\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
[1854]
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[]\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 5403--5406
[]\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
[1855] [1856]
Underfull \hbox (badness 3118) in paragraph at lines 5524--5526
[]\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
[1857]
Underfull \hbox (badness 2409) in paragraph at lines 5557--5561
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1858]
Underfull \hbox (badness 5091) in paragraph at lines 5661--5663
[]\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
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 
[1859]
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[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 5807--5811
[]\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 1708) in paragraph at lines 5807--5811
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the ap-pro-pri-ate bi-nary type where
Underfull \hbox (badness 2376) in paragraph at lines 5821--5828
[]\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 5821--5828
\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 5821--5828
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1861]
Underfull \hbox (badness 1314) in paragraph at lines 5880--5887
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5901--5906
[][][]\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 ,
[1862]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5922--5922
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
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[]\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
[1863]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6017--6017
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1864]
Underfull \hbox (badness 4132) in paragraph at lines 6098--6100
[]\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
[1865] [1866] [1867]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6256--6256
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1868] [1869]
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 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1870]
Underfull \hbox (badness 10000) in paragraph at lines 6439--6441
[]\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
[1871] [1872]
Underfull \hbox (badness 10000) in paragraph at lines 6580--6582
[]\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 6585--6587
[]\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
[1873] [1874] [1875]
Underfull \hbox (badness 1859) in paragraph at lines 6808--6811
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1876]
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[]\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 6901--6901
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
[1877]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6905--6905
 []\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 6913--6913
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1878] [1879] [1880] [1881]
Underfull \hbox (badness 10000) in paragraph at lines 7203--7205
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7208--7213
[]\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,
[1882] [1883]
Underfull \hbox (badness 10000) in paragraph at lines 7359--7364
[]\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 7359--7364
[][]\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
[1884]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7369
[]\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 7366--7369
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1885]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1886] [1887] [1888] [1889]
Underfull \hbox (badness 1789) in paragraph at lines 7758--7760
[]\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
[1890]
Underfull \hbox (badness 10000) in paragraph at lines 7816--7820
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1891] [1892]
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1893]
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1894] [1895] [1896] [1897]
Underfull \hbox (badness 5203) in paragraph at lines 8319--8322
[]\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
[1898]
Underfull \vbox (badness 4647) has occurred while \output is active [1899]
[1900]
Underfull \hbox (badness 1776) in paragraph at lines 8545--8552
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1901]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8569--8569
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1902] [1903]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8730--8730
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1904] [1905]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8911--8911
 []\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[] 
[1906] [1907]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8997--8997
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9000--9000
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9005--9005
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1908]
Underfull \hbox (badness 1077) in paragraph at lines 9077--9080
[]\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
[1909] [1910] [1911] [1912] [1913] [1914]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9517--9517
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1915]
Underfull \hbox (badness 10000) in paragraph at lines 9604--9606
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1916] [1917]
Underfull \hbox (badness 2181) in paragraph at lines 9727--9731
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 9727--9731
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 9739--9743
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1918]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9757--9757
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9761--9761
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1919] [1920]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9893--9893
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1921] [1922] [1923]
Underfull \hbox (badness 8075) in paragraph at lines 10093--10095
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
Underfull \hbox (badness 6725) in paragraph at lines 10143--10152
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 10143--10152
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 10143--10152
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1924] [1925]
Underfull \hbox (badness 3646) in paragraph at lines 10269--10271
[][][]$\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 /
[1926] [1927] [1928]
Underfull \hbox (badness 10000) in paragraph at lines 10447--10451
[]\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 10478--10484
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1929]
Underfull \hbox (badness 2012) in paragraph at lines 10573--10579
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1930]
Underfull \hbox (badness 2096) in paragraph at lines 10586--10588
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 10589--10591
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 10596--10599
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 10600--10603
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10654--10654
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
Underfull \hbox (badness 10000) in paragraph at lines 10661--10663
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
[1931]
Underfull \hbox (badness 1009) in paragraph at lines 10666--10677
[]\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
[1932]
Underfull \hbox (badness 2846) in paragraph at lines 10753--10763
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1933] [1934]
Underfull \hbox (badness 10000) in paragraph at lines 10902--10905
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1935]
Underfull \hbox (badness 2158) in paragraph at lines 10981--10984
[]\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
[1936] [1937] [1938]
Underfull \hbox (badness 3333) in paragraph at lines 11161--11163
[]\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-
[1939] [1940]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11322--11322
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1941]
Underfull \hbox (badness 5970) in paragraph at lines 11350--11353
[]\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 11350--11353
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11361--11370
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1942]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 11405--11405
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1943] [1944]
Underfull \hbox (badness 10000) in paragraph at lines 11529--11531
[]\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
[1945] [1946]
Underfull \hbox (badness 4492) in paragraph at lines 11683--11690
[]\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 11683--11690
\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 2452) in paragraph at lines 11683--11690
\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$"\T1/ptm/m/n/10 ) and
[1947] [1948]
Underfull \hbox (badness 2020) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1949]
Underfull \hbox (badness 10000) in paragraph at lines 11930--11933
[][][]$\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 11930--11933
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957]
Underfull \hbox (badness 4467) in paragraph at lines 12427--12429
[]\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 12440--12444
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 12454--12458
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 3557) in paragraph at lines 12460--12462
[]\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 passed to
Underfull \hbox (badness 1052) in paragraph at lines 12463--12465
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1958]
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 12514--12519
[]\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 12522--12525
[][][]\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 ,
[1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 12764--12767
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12780--12780
 []\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:[]
 
[1963]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12814--12814
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
Underfull \hbox (badness 1454) in paragraph at lines 12841--12845
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1964]
Underfull \hbox (badness 1715) in paragraph at lines 12866--12869
[]\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 12911--12913
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12923--12927
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1965] [1966] [1967]) [1968] [1969] [1970] (./KernSmooth-pkg.tex
Chapter 15.
[1971]
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) 
[1972] [1973] [1974] [1975] [1976]
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, 
[1977] [1978] [1979] [1980]) (./MASS-pkg.tex
Chapter 16.
[1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991]
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))[] 
[1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002]
[2003]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\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 2415--2415
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2015] [2016] [2017] [2018]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2019] [2020] [2021]
Underfull \hbox (badness 7362) in paragraph at lines 2863--2868
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/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/ptm/m/n/10 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2022] [2023]
Underfull \hbox (badness 4686) in paragraph at lines 3031--3033
[]\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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2024] [2025] [2026]
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
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[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2027]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038]
[2039]
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[]\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
[2040] [2041] [2042] [2043] [2044] [2045] [2046]
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 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2049]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2050] [2051] [2052] [2053] [2054]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
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[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2055]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2064]
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 []\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") 
[2065] [2066]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
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<to be read again> 
                   \relax 
l.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2067]
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[]\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
[2068] [2069] [2070] [2071]
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2073]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2074] [2075] [2076] [2077] [2078] [2079]
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 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2080]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\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 ) =
[2081]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2082] [2083]
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\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
[2084] [2085]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2086]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2087] [2088] [2089] [2090] [2091] [2092]
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[]\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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2093] [2094]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8123--8127
[]\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
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2115]
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[]\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),
[2116]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128] [2129]) (./Matrix-pkg.tex [2130]
Chapter 17.
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[]\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
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2131]
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[]\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
[2132]
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[]\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
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\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
[2133]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\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
[2134] [2135]
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 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2136]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\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
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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2137] [2138]
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[]\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 .
[2139] [2140] [2141]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2142]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
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\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
[2143]
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2144]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1094 ...- 'Matrix' S4 Generic and Methods}{chol}
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                   \relax 
l.1094 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2145pdfTeX 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.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:pdfTeX warning (ext4): des
tination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has b
een already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1176 \item[chol]
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l.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2146]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2147]
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[]\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
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[]\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
[2148]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
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 []\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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2149]
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[]\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
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\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
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[]\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
[2150]
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\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
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1583 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
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                   \relax 
l.1583 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1584 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
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                   \relax 
l.1605 \aliasA{rowMeans}{colSums}{rowMeans}
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                   \relax 
l.1616 \aliasA{rowSums}{colSums}{rowSums}
                                          [2151]
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[]\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
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\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
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[][][]\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
[2152]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2153]
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[]\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
[2154] [2155] [2156] [2157]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2158]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
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\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2159]
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[]\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
[2160]
Underfull \hbox (badness 10000) in paragraph at lines 2405--2408
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2161] [2162]
Underfull \hbox (badness 10000) in paragraph at lines 2507--2511
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2507--2511
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
Underfull \hbox (badness 2707) in paragraph at lines 2563--2567
[]\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 2568--2572
[]\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
[2163]
Underfull \hbox (badness 10000) in paragraph at lines 2575--2578
[]\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 ;
Underfull \hbox (badness 2689) in paragraph at lines 2628--2630
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2164]
Underfull \hbox (badness 1097) in paragraph at lines 2654--2657
[]\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''
[2165]
Underfull \hbox (badness 3646) in paragraph at lines 2902--2905
[]\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 2924--2925
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
Underfull \hbox (badness 1810) in paragraph at lines 2931--2933
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2934--2936
[]\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 3803) in paragraph at lines 2937--2941
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2166]
Underfull \hbox (badness 1371) in paragraph at lines 2946--2952
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 2953--2957
[]\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 2963--2967
[][][]\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
[2167] [2168]
Underfull \hbox (badness 1859) in paragraph at lines 3146--3148
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3191--3193
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2169] [2170]
Underfull \hbox (badness 1168) in paragraph at lines 3306--3309
[]\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
[2171]
Underfull \hbox (badness 4967) in paragraph at lines 3471--3475
[]\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
[2172]
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3476--3478
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
Underfull \hbox (badness 6364) in paragraph at lines 3518--3521
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2173] [2174]
Underfull \hbox (badness 10000) in paragraph at lines 3668--3673
[]\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 3668--3673
\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 10000) in paragraph at lines 3678--3680
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
Underfull \hbox (badness 10000) in paragraph at lines 3680--3683
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2175]
Underfull \hbox (badness 10000) in paragraph at lines 3788--3791
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 1735) in paragraph at lines 3788--3791
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
Underfull \hbox (badness 10000) in paragraph at lines 3791--3794
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 2318) in paragraph at lines 3791--3794
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2176]
Underfull \hbox (badness 6364) in paragraph at lines 3795--3798
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2177]
Underfull \hbox (badness 4060) in paragraph at lines 3915--3918
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2178]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3955--3955
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
Underfull \hbox (badness 3635) in paragraph at lines 4023--4027
[]\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
[2179]
Underfull \hbox (badness 10000) in paragraph at lines 4032--4035
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4032--4035
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4037--4041
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2180] [2181] [2182] [2183]
Underfull \hbox (badness 10000) in paragraph at lines 4325--4330
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2184] [2185]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4459--4459
 [] \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 4462--4462
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4476--4476
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2186] [2187]
Underfull \hbox (badness 10000) in paragraph at lines 4631--4633
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2188] [2189]
Underfull \hbox (badness 10000) in paragraph at lines 4778--4783
[]\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 ,
[2190]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4859--4859
 []\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 4861--4861
 []  \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 4865--4865
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4872--4872
 []  \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 '[] 
[2191] [2192]
Underfull \hbox (badness 4120) in paragraph at lines 5011--5014
[]\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
[2193]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5048--5048
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5053--5053
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5060--5060
 []\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 5063--5063
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2194]
Underfull \hbox (badness 1817) in paragraph at lines 5152--5161
[]\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 5637) in paragraph at lines 5194--5196
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2195]
Underfull \hbox (badness 3138) in paragraph at lines 5220--5222
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2196]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5284--5284
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5305--5307
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2197] [2198] [2199]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5542--5542
 []\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[] 
[2200]
Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[][][]\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 5634--5634
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2201]
Underfull \hbox (badness 1622) in paragraph at lines 5671--5676
[]\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 5671--5676
\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
[2202] [2203]
Underfull \hbox (badness 1062) in paragraph at lines 5857--5860
[]\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
[2204]
Underfull \hbox (badness 2809) in paragraph at lines 5886--5889
[]\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
[2205]
Underfull \hbox (badness 2635) in paragraph at lines 5998--6003
[]\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 5998--6003
\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 6006--6009
[]\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.,
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6127
\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 6117--6127
[][]\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
[2207]
Underfull \hbox (badness 1184) in paragraph at lines 6199--6202
[]\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
[2208]
Underfull \hbox (badness 10000) in paragraph at lines 6297--6300
[]\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.,
[2209]
Underfull \hbox (badness 10000) in paragraph at lines 6372--6375
[]\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 6388--6388
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2210]
Underfull \hbox (badness 2443) in paragraph at lines 6427--6433
[]\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 6427--6433
[][]\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 6448--6451
[]\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
[2211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6518--6518
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2212] [2213]
Underfull \hbox (badness 6268) in paragraph at lines 6654--6657
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2214]
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[]\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,
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\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2215]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
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                   \relax 
l.6771 \aliasA{det}{Matrix-class}{det}
                                      
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[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
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                   \relax 
l.6942 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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                   \relax 
l.7050 ...A{crossprod}{matrix-products}{crossprod}
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                   \relax 
l.7150 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2217]
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\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
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sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7310 \end{Details}
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l.7310 \end{Details}
                    ]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
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[]\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
[2221]
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[]\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
[2222]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2223]
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[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
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\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2224]
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
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[]\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 .
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\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
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[]\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.,
[2226] [2227]
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[]\T1/ptm/m/n/10 fast
[2228]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
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                   \relax 
l.8050 \HeaderA{norm}{Matrix Norms}{norm}
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h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
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                   \relax 
l.8050 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2229]
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[]\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 ,
[2230]
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[]\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
[2231]
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[]\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.,
[2232]
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[]\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.,
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2233] [2234]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2235]
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2236]
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[]\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
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2237]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
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                   \relax 
l.8829 \aliasA{qr}{qr-methods}{qr}
                                   [2238]
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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 []                  \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)),[] 
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 []          \T1/pcr/m/n/9 all.equal(qr.coef(qxr, y), cf <- c(int=6, b1=-3, c1=
-2, c2=-1), tol=1e-15)[] 
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 []          \T1/pcr/m/n/9 all.equal(unname(qcfXy), unname(cf), tol=1e-15) || #
 FAIL names: ## FIXME_______[] 
[2239]
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 []          \T1/pcr/m/n/9 all.equal(unname(m(qcfXY)), unname(m(cf)), tol=1e-15
) || # FAIL dimnames: ## FIXME_______[] 
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 []\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![] 
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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co
rrect colnames[] 
[2240]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\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
[2241]
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 []\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"[] 
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 
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 []\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
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<to be read again> 
                   \relax 
l.9116 ... the Reciprocal Condition Number}{rcond}
                                                   [2242] [2243]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2244] [2245] [2246]
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[]\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
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\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2247] [2248]
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[]\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
[2249]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
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<to be read again> 
                   \relax 
l.9691 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2251]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2252]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\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
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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2253]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\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,
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[]\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)
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\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
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\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
[2254]
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[]\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
[2255]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2256] [2257]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2258]
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[]\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
[2259]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\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 10445--10445
 []\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 10448--10448
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2260]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10471--10471
 []\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 10472--10472
 []\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)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10498--10498
 []\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 10500--10500
 []   \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 10502--10502
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2261]
Underfull \hbox (badness 10000) in paragraph at lines 10594--10602
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
Underfull \hbox (badness 1325) in paragraph at lines 10615--10619
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
Underfull \hbox (badness 10000) in paragraph at lines 10645--10649
[][][]\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
[2262]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10685 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2263]
Underfull \hbox (badness 1430) in paragraph at lines 10795--10797
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2264]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10821--10821
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2265]
Underfull \hbox (badness 2970) in paragraph at lines 10974--10980
[]\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 10974--10980
\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 11025--11028
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2266]
Underfull \hbox (badness 10000) in paragraph at lines 11047--11050
[]\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 11063--11068
[]\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 11074--11076
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2267] [2268]
Underfull \hbox (badness 3525) in paragraph at lines 11174--11178
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11181--11187
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 11275--11279
[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
Underfull \hbox (badness 1043) in paragraph at lines 11275--11279
[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
Underfull \hbox (badness 10000) in paragraph at lines 11291--11296
[]\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 1259) in paragraph at lines 11291--11296
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11299--11304
\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
[2270]
Underfull \hbox (badness 2057) in paragraph at lines 11371--11373
[]\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.,
[2271]
Underfull \hbox (badness 6641) in paragraph at lines 11457--11460
[]\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
[2272]
Underfull \hbox (badness 5133) in paragraph at lines 11497--11501
[]\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 11497--11501
\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
[2273]
Underfull \hbox (badness 7649) in paragraph at lines 11602--11604
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2274] [2275] [2276]
Underfull \hbox (badness 7362) in paragraph at lines 11797--11799
[]\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
[2277]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11835--11835
 []\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 11836--11836
 []\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)[] 
[2278] [2279]
Underfull \hbox (badness 6910) in paragraph at lines 12086--12088
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2280] [2281] [2282]) (./boot-pkg.tex
Chapter 18.
[2283] [2284] [2285] [2286] [2287] [2288] [2289]
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"), 
[2290]
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-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2291]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2292]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2293]
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 ,
[2294]
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 [2295]
[2296]
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
[2297]
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
[2298] [2299] [2300] [2301] [2302]
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-
[2303] [2304] [2305] [2306]
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), 
[2307] [2308] [2309] [2310]
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),[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2311]
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.
[2312] [2313] [2314] [2315]
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
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.
[2316]
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 ,
[2317]
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
[2318] [2319] [2320] [2321] [2322]
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,[] 
[2323] [2324] [2325]
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 ,
[2326]
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)) 
[2327] [2328] [2329]
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 
[2330] [2331] [2332] [2333] [2334] [2335] [2336]
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)[] 
[2337] [2338]
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])[] 
[2339] [2340] [2341]
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
[2342]
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 
[2343] [2344]
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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2345] [2346] [2347] [2348] [2349] [2350] [2351] [2352] [2353]
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
[2354] [2355] [2356] [2357]
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
[2358]
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])[] 
[2359] [2360] [2361] [2362] [2363] [2364] [2365] [2366]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2367]
Underfull \hbox (badness 1127) in paragraph at lines 5984--6002
\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
[2368]
Underfull \hbox (badness 2837) in paragraph at lines 6017--6020
[]\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
[2369] [2370] [2371] [2372]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6302--6302
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2373] [2374]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6491--6491
 []\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 6493--6493
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2375] [2376] [2377]
Underfull \hbox (badness 1596) in paragraph at lines 6738--6742
[]\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
[2378] [2379]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6898--6898
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387]) (./class-pkg.tex
[2388]
Chapter 19.
[2389] [2390] [2391] [2392] [2393] [2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404]) (./cluster-pkg.tex
Chapter 20.
[2405]
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[]\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-
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\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
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\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
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\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
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\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2406]
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[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2407]
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 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
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 []  \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]))[] 
[2408] [2409]
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[2411]
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 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
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 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2412]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2413]
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 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2414]
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[]\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
[2415]
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[][][]\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 
,
[2416]
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 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2417]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
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 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, d.power = 1, verbose =
 interactive(), ...) 
[2418]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2419] [2420]
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 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2421]
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[]\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
[2422]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1212--1212
 []          \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 1218--1218
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2423] [2424]
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[2425]
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[][][]\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 1443--1443
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
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 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1460--1460
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2426]
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[]\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
[2427] [2428]
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\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
[2429]
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 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
[2430]
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 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2431] [2432] [2433] [2434]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
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[][][]\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.
[2435] [2436] [2437]
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[][][]\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 ,
[2438]
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[]\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
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[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
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[][][]\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 ,
[2439] [2440] [2441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2573--2573
 []\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 ):[] 
[2442] [2443] [2444]
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[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
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 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2445] [2446]
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 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2447] [2448] [2449]
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 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
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 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2450]
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[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2451]
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 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
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 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2452] [2453] [2454]
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[]\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
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[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2455]
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[][][]\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 ,
[2456]
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[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 which 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
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[][][]\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 ,
[2457] [2458] [2459]
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[][][]\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 3770--3773
[][][]\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 ,
[2460]
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 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
[2461]
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[]\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
[2462] [2463] [2464]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4027--4027
 []     \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 4029--4029
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4058--4063
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2465]
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\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2466]
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 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
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 []   \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 4178--4178
 []      \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 4181--4181
 []\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 4183--4183
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
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 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2475]
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[]\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
[2476]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2477] [2478] [2479]) (./foreign-pkg.tex [2480]
Chapter 22.
[2481]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2482] [2483]
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[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2484]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2485] [2486] [2487]
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 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2488]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2489]
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[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2490] [2491] [2492]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2493]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2494]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2495] [2496]
Underfull \hbox (badness 10000) in paragraph at lines 994--995
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2497] [2498]
Underfull \hbox (badness 1286) in paragraph at lines 1115--1119
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2499]
Underfull \hbox (badness 10000) in paragraph at lines 1188--1194
[]\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 ,
[2500]) (./lattice-pkg.tex
Chapter 23.
[2501] [2502] [2503]
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"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2504]
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 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2505]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
Underfull \hbox (badness 10000) in paragraph at lines 357--369
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2506]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2507] [2508]
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[]\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
[2509] [2510] [2511] [2512]
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
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2513]
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
[2514] [2515]
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
[2516] [2517] [2518]
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 ,
[2519]
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 ,
[2520]
Underfull \vbox (badness 10000) has occurred while \output is active [2521]
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
[2522]
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
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[]\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
[2523]
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
[2524] [2525] [2526]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2527]
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
[2528] [2529] [2530]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2531] [2532] [2533]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2534] [2535]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2536]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2537]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\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 2793--2798
\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 2879--2883
[]\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 2879--2883
\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 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2538]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\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 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
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\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 2961--2965
[]\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
[2539] [2540]
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 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
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 []      \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 3064--3064
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2541]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\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 3145--3152
\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
[2542] [2543] [2544] [2545]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2546]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2547] [2548] [2549] [2550] [2551]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2552]
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\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2553] [2554]
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 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
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[]\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
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[]\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 4107--4111
\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
[2555]
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[]\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 4172--4176
\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
[2556] [2557]
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[]\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 ,
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\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 4286--4296
\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
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\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
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\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
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[]\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 ,
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[]\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
[2558] [2559] [2560] [2561] [2562] [2563]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2564] [2565]
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[]\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 .
[2566] [2567]
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[]\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
[2568] [2569] [2570] [2571] [2572] [2573]
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[][][]\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
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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2574]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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\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
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[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
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\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
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\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2575]
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[]\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
[2576]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2577]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2578]
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2579]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\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
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[]\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 5859--5866
\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
[2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\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 ,
[2582] [2583]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2584] [2585]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\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 6275--6280
\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
[2586] [2587]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2588]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\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
[2589]
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[]\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 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2590]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
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\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2591] [2592] [2593] [2594] [2595]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\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 6957--6964
\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
[2596]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2597]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
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\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
[2598]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\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
[2599] [2600]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2601]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2602] [2603]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
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[]\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
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\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
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\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
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\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2604]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2605]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2606] [2607] [2608]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2609]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\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
Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2610] [2611] [2612] [2613] [2614] [2615] [2616] [2617]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\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 8467--8470
\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
[2618] [2619]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
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 []\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 8655--8655
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2620]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\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
[2621]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2622]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2623] [2624]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2625] [2626]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2627]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\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
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\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
[2628] [2629] [2630] [2631] [2632] [2633] [2634]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\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 4518) in paragraph at lines 9619--9623
\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 ,
Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2635] [2636] [2637]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2638] [2639] [2640] [2641])
(./mgcv-pkg.tex [2642]
Chapter 24.
Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2643] [2644]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
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 []    \T1/pcr/m/n/10 sparse=FALSE,cluster=NULL,nthreads=NA,gc.level=1,use.chol
=FALSE,[] 
[2645]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2646] [2647] [2648] [2649]
Underfull \hbox (badness 10000) in paragraph at lines 368--375
[][][]\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 368--375
[][]\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 368--375
[][]\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 ,
[2650] [2651] [2652] [2653]
Underfull \hbox (badness 2922) in paragraph at lines 611--612
[]\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
[2654]
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[]\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
[2655] [2656] [2657] [2658] [2659] [2660] [2661]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2662]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1103--1103
 []\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)[] 
[2663] [2664] [2665] [2666] [2667] [2668]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2669] [2670] [2671] [2672] [2673] [2674]
Underfull \hbox (badness 1052) in paragraph at lines 1879--1887
\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
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1900--1900
 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 
Underfull \hbox (badness 1728) in paragraph at lines 1907--1910
[]\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
[2675]
Underfull \hbox (badness 1142) in paragraph at lines 1920--1924
\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 1946--1951
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2676] [2677] [2678]
Underfull \hbox (badness 1043) in paragraph at lines 2106--2112
\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
[2679]
Underfull \hbox (badness 10000) in paragraph at lines 2233--2239
[][][]\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 2233--2239
[][]\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 2233--2239
[][]\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 ,
[2680] [2681]
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[2684] [2685] [2686] [2687] [2688] [2689] [2690]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2862--2862
 []         \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 2865--2865
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2691] [2692] [2693] [2694] [2695]
Underfull \hbox (badness 5189) in paragraph at lines 3180--3184
[]\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
[2696]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 3297--3297
 []\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 [2698]
[2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3867--3867
 []  \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)+[] 
[2707] [2708]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2709] [2710] [2711]
Underfull \hbox (badness 5970) in paragraph at lines 4197--4203
[][][]\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 ,
[2712]
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[2714] [2715]
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[]\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 4469--4470
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
[2725]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2726] [2727] [2728]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5664--5664
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744]
Underfull \hbox (badness 1242) in paragraph at lines 6197--6198
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2745] [2746] [2747]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
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[2766]
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[]\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 7497--7500
\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 7497--7500
\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 .
[2767]
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[]\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 7553--7556
\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
[2768] [2769] [2770]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 
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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2771] [2772] [2773]
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\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
[2774] [2775] [2776]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2777] [2778] [2779] [2780] [2781] [2782]
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 []  \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[] 
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
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[]\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
[2784]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2785]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\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,
[2786] [2787] [2788]
Underfull \hbox (badness 1253) in paragraph at lines 8860--8862
[]\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,
[2789] [2790] [2791]
Underfull \hbox (badness 1946) in paragraph at lines 9038--9045
[]\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
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\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
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[]\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 9046--9049
\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.
[2792]
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 []\T1/pcr/m/n/9 ## see also examples for gam.models, gam.vcomp, gamm and smoot
h.construct.re.smooth.spec 
[2793]
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[]\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 ,
[2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] [2803] [2804]
[2805]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
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[]\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
[2806]
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\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 .
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\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
[2807]
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\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 9940--9944
\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 ,
[2808] [2809]
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[][][]\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
[2811]
Underfull \hbox (badness 10000) in paragraph at lines 10176--10177
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2812] [2813]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2814]
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 []  \T1/pcr/m/n/9 sm <- smoothCon(s(x,bs="bs",m=m,k=k),data.frame(x),scale.pen
alty=FALSE)[[1]][] 
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
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\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
[2815] [2816] [2817]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2818]
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 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
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 []\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[] 
[2819]
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\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2820] [2821]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2822] [2823] [2824] [2825]
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 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 11038--11040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2826] [2827]
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Underfull \hbox (badness 10000) in paragraph at lines 11197--11200
[]\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 11197--11200
\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 11197--11200
\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"
[2829] [2830]
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 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 11324--11330
\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-
[2831] [2832] [2833]
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 []\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...[] 
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 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 11541--11541
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 
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 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 
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 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2836]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2837] [2838] [2839] [2840]
Underfull \hbox (badness 3396) in paragraph at lines 11929--11934
[][][]\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
[2841]
Underfull \hbox (badness 10000) in paragraph at lines 11974--11976
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2842] [2843] [2844] [2845]
Underfull \hbox (badness 10000) in paragraph at lines 12170--12173
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
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\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
Underfull \hbox (badness 10000) in paragraph at lines 12203--12207
[][][]\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 12203--12207
[][]\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 12203--12207
[][]\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 ,
[2846] [2847] [2848]
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[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2849]
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 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2850] [2851]
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 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2852] [2853] [2854]
Underfull \hbox (badness 4846) in paragraph at lines 12708--12711
[]\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
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[2861] [2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869]
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 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2870] [2871] [2872] [2873] [2874]
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 []\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 13969--13969
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
[2875]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13981--13981
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2876] [2877]) (./nlme-pkg.tex [2878]
Chapter 25.
[2879]
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
[2880]
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
[2881] [2882] [2883] [2884] [2885]
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,[] 
[2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895]
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"),[] 
[2896]
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
[2897] [2898] [2899] [2900] [2901] [2902] [2903]
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 ,
[2904]
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
[2905] [2906] [2907] [2908] [2909]
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 ,
[2910]
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")[] 
[2911]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2912] [2913]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[2914]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2915] [2916] [2917] [2918] [2919] [2920] [2921] [2922]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933]
[2934]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4345--4345
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2946] [2947] [2948] [2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956]
[2957] [2958]
Underfull \hbox (badness 10000) in paragraph at lines 5155--5159
[][][]\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 ,
[2959] [2960] [2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 5472--5476
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5472--5476
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2964] [2965]
Underfull \hbox (badness 10000) in paragraph at lines 5587--5590
[][][]\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 ,
[2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
Underfull \hbox (badness 2799) in paragraph at lines 6093--6099
\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
[2975]
Underfull \hbox (badness 7133) in paragraph at lines 6154--6158
[]\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 ,
[2976]
Underfull \hbox (badness 2057) in paragraph at lines 6238--6249
[][][]\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 ,
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6306
[]\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 6336--6336
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2978] [2979] [2980] [2981]
Underfull \hbox (badness 7133) in paragraph at lines 6554--6558
[]\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 ,
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 6653--6659
[][][]\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 ,
[2983]
Underfull \hbox (badness 10000) in paragraph at lines 6719--6721
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2984]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6749--6749
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2985] [2986] [2987]
Underfull \hbox (badness 10000) in paragraph at lines 6992--6999
[][][]\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 ,
[2988]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7009--7009
 []                \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
[2989] [2990] [2991]
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 ,
[2992] [2993] [2994]
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 1817) 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 
20 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 ,
[2995] [2996] [2997]
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
[2998] [2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 1642) in paragraph at lines 8036--8058
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3004] [3005]
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
[3006] [3007] [3008] [3009] [3010]
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 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3011]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3012] [3013] [3014]
Underfull \hbox (badness 10000) in paragraph at lines 8722--8734
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9320
[][][]\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 9324--9324
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3024]
Underfull \hbox (badness 6300) in paragraph at lines 9406--9409
[]\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
[3025] [3026] [3027] [3028]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9675 ...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.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3029]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
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[]\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 9739--9742
\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
[3030] [3031] [3032]
Underfull \hbox (badness 2435) in paragraph at lines 9913--9918
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 7291) in paragraph at lines 10203--10205
[]\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
[3038] [3039] [3040]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3041]
Underfull \hbox (badness 1596) in paragraph at lines 10448--10474
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3042] [3043] [3044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3045] [3046]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
[3047]
Underfull \hbox (badness 10000) in paragraph at lines 10823--10825
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10835--10838
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10858--10858
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060] [3061] [3062]
Underfull \hbox (badness 6268) in paragraph at lines 11890--11900
[][][]\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 ,
[3063] [3064] [3065] [3066]
Underfull \hbox (badness 10000) in paragraph at lines 12151--12157
[][][]\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 ,
[3067] [3068] [3069] [3070] [3071]
Underfull \hbox (badness 6876) in paragraph at lines 12473--12475
[]\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
[3072] [3073]
Underfull \hbox (badness 2452) in paragraph at lines 12629--12636
[][][]\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 ,
[3074]
Underfull \hbox (badness 10000) in paragraph at lines 12694--12700
[][][]\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 ,
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
[3086] [3087] [3088] [3089]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13646--13646
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
Underfull \hbox (badness 10000) in paragraph at lines 13673--13676
[]\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
[3090]
Underfull \hbox (badness 6016) in paragraph at lines 13701--13704
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13701--13704
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13708--13711
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13716--13723
[]\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 13716--13723
\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
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13773--13773
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13780--13783
[]\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 13780--13783
\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
[3092]
Underfull \hbox (badness 4582) in paragraph at lines 13808--13811
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13808--13811
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13812--13815
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3093]
Underfull \hbox (badness 10000) in paragraph at lines 13888--13891
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13913--13920
\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 ,
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 13982--13984
[][][]\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 ,
[3095] [3096] [3097]
Underfull \hbox (badness 1540) in paragraph at lines 14197--14202
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
[3098]
Underfull \hbox (badness 1215) in paragraph at lines 14244--14246
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3099] [3100] [3101] [3102] [3103]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14488--14488
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]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.15144 ...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.15144 ...Extract Random Effects}{random.effects}
                                                   [3113] [3114] [3115]
[3116] [3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1009) in paragraph at lines 15801--15810
\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
[3123] [3124] [3125]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15948--15948
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3126] [3127] [3128] [3129]
Underfull \hbox (badness 10000) in paragraph at lines 16226--16244
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16226--16244
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3130]
Underfull \hbox (badness 10000) in paragraph at lines 16283--16289
[][][]\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 ,
[3131]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16314--16314
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3132] [3133] [3134] [3135] [3136] [3137] [3138]
Underfull \hbox (badness 1728) in paragraph at lines 16798--16801
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3139] [3140] [3141] [3142] [3143]
Underfull \hbox (badness 1867) in paragraph at lines 17131--17140
\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 17131--17140
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3144]
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\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 ,
[3145] [3146] [3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 17442--17449
[][][]\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 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156]
Underfull \hbox (badness 10000) in paragraph at lines 17972--17982
[][][]\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 17972--17982
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18010--18015
\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
[3157]
Underfull \hbox (badness 3579) in paragraph at lines 18074--18079
\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
[3158]
Underfull \hbox (badness 3579) in paragraph at lines 18137--18142
\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
[3159]
Underfull \hbox (badness 1577) in paragraph at lines 18198--18200
[]\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 18200--18205
\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
[3160]
Underfull \hbox (badness 3579) in paragraph at lines 18263--18268
\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
[3161]
Underfull \hbox (badness 10000) in paragraph at lines 18296--18305
[][][]\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 18296--18305
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18335--18340
\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
[3162] [3163] [3164]
Underfull \hbox (badness 1009) in paragraph at lines 18484--18493
\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
[3165] [3166]
Underfull \hbox (badness 1009) in paragraph at lines 18618--18627
\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
[3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174]) (./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}
                                                   [3175]
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,[] 
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3176] [3177] [3178]
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,[] 
[3179]
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)[] 
[3180]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3181]
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,[] 
[3182]) (./rpart-pkg.tex
Chapter 27.
[3183] [3184] [3185] [3186]
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, ...)[] 
[3187]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3188] [3189] [3190]
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
[3191] [3192]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3193]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3194]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3195]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3196] [3197] [3198]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3199]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3200]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\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 1286--1286
 []\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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3201] [3202] [3203] [3204] [3205] [3206]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3207] [3208]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3209] [3210] [3211]) (./spatial-pkg.tex [3212]
Chapter 28.
[3213] [3214] [3215] [3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3219] [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
[3230] [3231]) (./survival-pkg.tex [3232]
Chapter 29.
[3233] [3234]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
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 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
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 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3235]
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 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
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 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... 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
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                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3236] [3237]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3238]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3239] [3240] [3241]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3242] [3243]
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 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3244] [3245] [3246]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
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on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1040 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3248] [3249] [3250]
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
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 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3259] [3260] [3261] [3262]
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 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3263] [3264] [3265] [3266]
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 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3267]
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[]\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
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[]\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
[3268]
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 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 
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 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3269] [3270] [3271] [3272] [3273]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3274] [3275] [3276]
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 []                    \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 )))[] 
[3277] [3278] [3279] [3280]
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[3282] [3283]
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 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3284] [3285]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3286] [3287]
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 []\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[] 
[3288]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3289] [3290] [3291]
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[]\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
[3292] [3293]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3294] [3295]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3296]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3297]
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 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
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 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3298] [3299]
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 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3300] [3301] [3302] [3303]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
[3304]
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3305] [3306]
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 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
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 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
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 []    \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 ),[] 
[3314] [3315] [3316] [3317]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3318]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3319]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3320]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3321]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3322] [3323] [3324]
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[][][]\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 ,
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3325] [3326]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3327] [3328]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3329] [3330]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3331] [3332] [3333]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3334]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3335] [3336]
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\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 .
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\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 ,
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\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
[3337]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3338] [3339] [3340]
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 []                 \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 )[] 
[3341] [3342]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \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 )[] 
[3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3347] [3348] [3349] [3350] [3351]) [3352]
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'.
 )
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(/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]
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Chapter 1.
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
char-ac-ter vec-tors. The first en-try is al-ways
[4]
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[]\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
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\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base 
^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \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,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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[]\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 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if
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\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6] [7]
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[][][]\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]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
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[]\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]
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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19]
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[]\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
[20] [21] [22] [23]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
 of
[27]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[28]
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[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then
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[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[29] [30]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())
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[]\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]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[35] [36]
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[]\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
[37] [38] [39] [40] [41]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
Underfull \hbox (badness 10000) in paragraph at lines 2650--2655
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[56] [57] [58] [59] [60] [61]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\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
[62] [63] [64]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[65] [66]
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 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[67]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
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\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[68]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[69] [70] [71] [72]
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[]\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
[73] [74] [75] [76] [77] [78]
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[]\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
[79] [80] [81] [82] [83] [84] [85] [86]
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[]\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 : / /
[87] [88] [89]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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 []\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}[] 
[90] [91]
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[]\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
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[]\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
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\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
[92] [93]
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[94]
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[]\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 : 
[95] [96]
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[]\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
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\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
[97] [98]
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\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[99]
Underfull \hbox (badness 1067) in paragraph at lines 6660--6667
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[100] [101]
Underfull \vbox (badness 10000) has occurred while \output is active [102]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6837--6837
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[103] [104] [105] [106]
Underfull \hbox (badness 10000) in paragraph at lines 7168--7170
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[107] [108]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7313--7313
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[109]
Underfull \hbox (badness 4595) in paragraph at lines 7355--7358
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[110] [111] [112]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7551--7551
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[113] [114]
Underfull \hbox (badness 8132) in paragraph at lines 7652--7656
[]\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 7652--7656
\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 7671--7682
[]\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 1062) in paragraph at lines 7671--7682
[][]\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
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7704--7708
[]\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")
[115] [116] [117] [118] [119] [120]
Underfull \hbox (badness 10000) in paragraph at lines 8146--8158
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8146--8158
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[121] [122] [123]
Underfull \hbox (badness 5802) in paragraph at lines 8351--8355
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[124] [125]
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\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
Underfull \hbox (badness 10000) in paragraph at lines 8528--8532
[]\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
[126] [127]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8618--8618
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[128] [129]
Underfull \hbox (badness 4254) in paragraph at lines 8779--8783
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[130]
Underfull \hbox (badness 1132) in paragraph at lines 8839--8846
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[131] [132]
Underfull \hbox (badness 1603) in paragraph at lines 8952--8955
[]\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
[133] [134] [135] [136] [137] [138] [139] [140]
Underfull \hbox (badness 1917) in paragraph at lines 9540--9545
[]\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
[141]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9595--9595
 []\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 9596--9596
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[142] [143]
Underfull \hbox (badness 1168) in paragraph at lines 9698--9703
\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
[144] [145]
Underfull \hbox (badness 2828) in paragraph at lines 9836--9840
[][][]$\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 9836--9840
\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 _
[146] [147] [148]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10067--10067
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[149]
Underfull \hbox (badness 1629) in paragraph at lines 10141--10145
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[150] [151]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 10254--10262
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10263--10265
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[152]
Underfull \hbox (badness 3735) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[153] [154]
Underfull \hbox (badness 10000) in paragraph at lines 10490--10493
[]\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
[155] [156] [157] [158] [159] [160] [161] [162] [163]
Underfull \hbox (badness 5288) in paragraph at lines 11156--11158
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11166--11171
[]\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
[164]
Underfull \hbox (badness 10000) in paragraph at lines 11224--11226
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[165] [166]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\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 11341--11345
\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
[167] [168]
Underfull \hbox (badness 10000) in paragraph at lines 11456--11458
[]\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
Underfull \hbox (badness 2790) in paragraph at lines 11499--11501
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[169] [170] [171]
Underfull \hbox (badness 4048) in paragraph at lines 11669--11679
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 11669--11679
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[172] [173] [174]
Underfull \hbox (badness 5460) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[175] [176] [177] [178] [179]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 12280--12280
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[180] [181] [182] [183]
Underfull \hbox (badness 5119) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[184] [185]
Underfull \hbox (badness 2221) in paragraph at lines 12703--12709
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[186] [187] [188]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[189] [190]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[191] [192]
Underfull \hbox (badness 10000) in paragraph at lines 13205--13207
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[193] [194]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\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 (30.78088pt too wide) in paragraph at lines 13355--13355
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[195] [196]
Underfull \hbox (badness 10000) in paragraph at lines 13447--13450
[][][]\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 (4.38043pt too wide) in paragraph at lines 13457--13457
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[197]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 7238) in paragraph at lines 13569--13576
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 13569--13576
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 13569--13576
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
[198] [199] [200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13740--13740
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13741--13741
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[201] [202]
Underfull \hbox (badness 10000) in paragraph at lines 13820--13824
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 13820--13824
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[203] [204]
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 []\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 13971--13971
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[205]
Underfull \hbox (badness 1168) in paragraph at lines 14055--14059
[]\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 14055--14059
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[206]
Underfull \hbox (badness 6944) in paragraph at lines 14149--14152
[][][]\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 ,
[207]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14174--14174
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14308--14310
[]\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 14327--14327
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14329--14329
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14332--14332
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
Underfull \hbox (badness 2790) in paragraph at lines 14338--14341
[]\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 4254) in paragraph at lines 14354--14362
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14369--14373
[]\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
[210]
Underfull \hbox (badness 10000) in paragraph at lines 14430--14432
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\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,
Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14441--14449
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[212]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14545--14545
 []\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 ")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [213]
[214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225]
[226]
Underfull \hbox (badness 2418) in paragraph at lines 15479--15483
\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 15486--15489
[]\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 15514--15521
[][][]\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 ,
[227] [228] [229] [230]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[231] [232] [233] [234]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16024--16024
 []  \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 16053--16053
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [235]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16104--16104
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
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[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16110--16114
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[236] [237] [238] [239]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16453--16453
 []\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))) 
[240] [241] [242] [243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16703--16703
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[244] [245] [246] [247]
Underfull \hbox (badness 2435) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
Underfull \hbox (badness 1867) in paragraph at lines 17006--17013
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17006--17013
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17006--17013
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
[248]
Underfull \hbox (badness 2285) in paragraph at lines 17021--17023
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17029--17029
 []\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.[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17039--17039
 []    \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 17059--17059
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[249] [250] [251] [252] [253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17520--17522
[]\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
[256]
Underfull \hbox (badness 4217) in paragraph at lines 17604--17613
[][][]\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 17619--17635
[][][]\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 ,
[257] [258] [259] [260] [261] [262]
Underfull \hbox (badness 4699) in paragraph at lines 18033--18036
[]\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 ,
[263] [264]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[265] [266]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[267] [268] [269] [270] [271] [272]
Underfull \hbox (badness 1430) in paragraph at lines 18700--18705
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 18700--18705
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[273]
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[274]
Underfull \hbox (badness 10000) in paragraph at lines 18821--18828
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 18821--18828
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 18821--18828
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
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\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 18837--18839
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[275] [276]
Underfull \hbox (badness 1975) in paragraph at lines 18909--18912
[]\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
[277] [278] [279] [280] [281]
Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\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
[283] [284]
Underfull \hbox (badness 10000) in paragraph at lines 19475--19479
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\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
[285]
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[][][]\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 ,
[286] [287]
Underfull \hbox (badness 10000) in paragraph at lines 19692--19696
[]\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
[288]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\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 19747--19752
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 19747--19752
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[289] [290] [291]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19913--19913
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Underfull \hbox (badness 3343) in paragraph at lines 19973--19977
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[292] [293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20059--20059
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[294] [295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20180--20180
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (85.38034pt too wide) in paragraph at lines 20183--20183
 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects
 w/ same name in .GlobalEnv[] 
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[296]
Underfull \hbox (badness 10000) in paragraph at lines 20256--20259
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1337) in paragraph at lines 20285--20292
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 2229) in paragraph at lines 20285--20292
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
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\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
Underfull \hbox (badness 2564) in paragraph at lines 20304--20307
[]\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
[297]
Underfull \hbox (badness 1205) in paragraph at lines 20357--20362
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[298] [299] [300] [301]
Underfull \hbox (badness 2469) in paragraph at lines 20667--20673
[]\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 1939) in paragraph at lines 20667--20673
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 20667--20673
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[302] [303] [304] [305] [306]
Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 1655) in paragraph at lines 21382--21386
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[313] [314] [315] [316]
Underfull \hbox (badness 2277) in paragraph at lines 21628--21631
[]\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.
[317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 10000) in paragraph at lines 22108--22114
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
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\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
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[]\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 2951) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22140--22148
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[324] [325]
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 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[326]
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[327] [328] [329] [330] [331] [332]
Underfull \hbox (badness 10000) in paragraph at lines 22707--22715
\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 ;
[333]
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[]\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
[334]
Underfull \hbox (badness 7308) in paragraph at lines 22898--22904
[]\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 5077) in paragraph at lines 22898--22904
\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 10000) in paragraph at lines 22908--22911
[]\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 22908--22911
\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
[335] [336] [337]
Underfull \hbox (badness 10000) in paragraph at lines 23060--23062
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[338] [339] [340] [341] [342] [343] [344] [345] [346]
Underfull \hbox (badness 2197) in paragraph at lines 23722--23726
[]\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 23722--23726
\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
[347]
Underfull \hbox (badness 2846) in paragraph at lines 23736--23740
[]\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 23736--23740
\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
[348]
Underfull \hbox (badness 10000) in paragraph at lines 23826--23832
[]\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 23826--23832
\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 23839--23841
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[349]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 23890--23890
 [] \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:[] 
[350] [351]
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[352] [353]
Underfull \hbox (badness 4120) in paragraph at lines 24152--24159
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[354]
Underfull \hbox (badness 1694) in paragraph at lines 24288--24291
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[355] [356] [357] [358]
Underfull \hbox (badness 1603) in paragraph at lines 24527--24529
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[359]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 24645--24653
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[360]
Underfull \hbox (badness 5475) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[361]
Underfull \hbox (badness 3271) in paragraph at lines 24764--24767
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[362]
Overfull \vbox (2.42159pt too high) has occurred while \output is active
[363]
Underfull \hbox (badness 3138) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[364]
Underfull \hbox (badness 1194) in paragraph at lines 25047--25050
[]\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 25071--25073
[]\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 25083--25087
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25083--25087
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25088--25094
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25109--25120
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25121--25124
[]\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
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
[]\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 25145--25152
[]\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 10000) in paragraph at lines 25145--25152
\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
Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 25145--25152
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[366] [367] [368] [369]
Underfull \vbox (badness 10000) has occurred while \output is active [370]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25478--25478
 []\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 25491--25495
[]\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 25491--25495
\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)]
[371] [372] [373] [374]
Underfull \hbox (badness 4341) in paragraph at lines 25814--25816
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[375]
Underfull \hbox (badness 4518) in paragraph at lines 25850--25856
[][][]\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
Overfull \hbox (42.18039pt too wide) in paragraph at lines 25872--25872
 []\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 25884--25884
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[376] [377] [378] [379] [380] [381] [382]
Underfull \hbox (badness 10000) in paragraph at lines 26306--26310
[]\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,
[383]
Underfull \hbox (badness 1796) in paragraph at lines 26369--26372
[]\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
[384] [385] [386]
Underfull \hbox (badness 10000) in paragraph at lines 26564--26567
[]\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
[387] [388] [389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 1226) in paragraph at lines 27186--27191
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[396]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27231--27231
 []           \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))[] 
[397] [398] [399] [400]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27497--27497
 []\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 27508--27508
 []\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 27514--27514
 []\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 27515--27515
 []\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 27518--27518
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[401]
Underfull \hbox (badness 7415) in paragraph at lines 27593--27597
[]\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
[402]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27614--27614
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[403]
Underfull \hbox (badness 2418) in paragraph at lines 27762--27773
[]\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
[404] [405]
Underfull \hbox (badness 1248) in paragraph at lines 27886--27893
\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 27886--27893
\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 /
[406]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[407] [408]
Underfull \hbox (badness 1337) in paragraph at lines 28092--28095
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[409]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 28140--28140
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 28157--28168
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 28169--28172
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[410] [411]
Underfull \hbox (badness 1117) in paragraph at lines 28264--28270
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 4048) in paragraph at lines 28639--28644
[]\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 28639--28644
\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 28639--28644
\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 ,
[418] [419] [420] [421] [422] [423] [424] [425]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29177--29177
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[426] [427] [428] [429]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 29460--29462
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[430] [431]
Underfull \hbox (badness 7558) in paragraph at lines 29676--29680
[]\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 29686--29688
[]\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
[432]
Underfull \hbox (badness 5417) in paragraph at lines 29691--29694
[][][]\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 29695--29697
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[433] [434] [435] [436] [437] [438]
Underfull \hbox (badness 10000) in paragraph at lines 30105--30109
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[451] [452] [453]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[454]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31206--31206
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[455]
Underfull \hbox (badness 1158) in paragraph at lines 31310--31315
[]\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
[456]
Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 31337--31343
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[457]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 31413--31418
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[458]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31495--31495
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[459] [460] [461]
Underfull \hbox (badness 2809) in paragraph at lines 31759--31765
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 31766--31769
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473]
Underfull \hbox (badness 1735) in paragraph at lines 32578--32584
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[474]
Underfull \hbox (badness 4303) in paragraph at lines 32594--32597
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[475] [476] [477] [478] [479]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 32915--32915
 []         \T1/pcr/m/n/10 method = c("shell", "quick", "radix"), index.return 
= FALSE)[] 
[480] [481] [482]
Underfull \hbox (badness 2512) in paragraph at lines 33187--33189
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[483] [484] [485] [486]
Underfull \vbox (badness 10000) has occurred while \output is active [487]
[488]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33581--33581
 []\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)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33596--33596
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[489] [490] [491] [492] [493] [494]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34031--34031
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34032--34032
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[495] [496] [497]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 34238--34238
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[498]
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 34322--34332
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[499]
Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 1728) in paragraph at lines 34379--34386
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 34379--34386
\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 34379--34386
\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
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[504] [505] [506]
Underfull \hbox (badness 1163) in paragraph at lines 34851--34858
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 34851--34858
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[507] [508] [509] [510]
Underfull \hbox (badness 1142) in paragraph at lines 35123--35129
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 35138--35138
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[511] [512] [513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35384--35384
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[514]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35428--35428
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[515] [516] [517] [518] [519] [520] [521]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 35860--35860
 []\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 35863--35863
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[522]
Underfull \hbox (badness 10000) in paragraph at lines 35908--35911
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35955--35955
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[523] [524] [525] [526]
Underfull \hbox (badness 2762) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[527]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 36252--36252
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[528] [529]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36417--36417
 []\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. 
[530]
Underfull \hbox (badness 3219) in paragraph at lines 36500--36505
[]\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 36500--36505
\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
[531] [532]
Underfull \hbox (badness 2452) in paragraph at lines 36590--36593
\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 36590--36593
\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
[533] [534]
Underfull \hbox (badness 10000) in paragraph at lines 36777--36781
[]\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
[535]
Underfull \hbox (badness 1584) in paragraph at lines 36792--36795
[]\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
[536] [537] [538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36985--36985
 []\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 
[539] [540]
Underfull \hbox (badness 1082) in paragraph at lines 37120--37123
[]\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
[541] [542] [543]
Underfull \hbox (badness 1038) in paragraph at lines 37308--37311
[]\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
[544] [545] [546] [547] [548]
Underfull \hbox (badness 1515) in paragraph at lines 37647--37650
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[549] [550]
Underfull \hbox (badness 1924) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[551]
Underfull \hbox (badness 4096) in paragraph at lines 37869--37872
[]\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 ,
[552] [553] [554]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38103--38103
 []            \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 38105--38105
 []            \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),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 38107--38107
 []                 \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)))))[] 
[555]
Underfull \hbox (badness 10000) in paragraph at lines 38120--38122
[]\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
[556]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[557] [558]
Underfull \hbox (badness 1867) in paragraph at lines 38318--38322
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 38380--38384
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[559] [560] [561] [562] [563]
Underfull \hbox (badness 1371) in paragraph at lines 38726--38730
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val
id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z
one col-
Underfull \hbox (badness 1648) in paragraph at lines 38726--38730
\T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see []
[]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _
[564]
Underfull \hbox (badness 5637) in paragraph at lines 38799--38808
[]\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 Ol-son/IANA
Underfull \hbox (badness 1629) in paragraph at lines 38799--38808
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 38809--38816
[]\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 38809--38816
\T1/ptm/m/n/10 fault on OS X and Win-dows: rec-om-mended on So-laris), the data
base at
Underfull \hbox (badness 1303) in paragraph at lines 38809--38816
\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 '
[565]
Underfull \hbox (badness 10000) in paragraph at lines 38873--38875
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / www . twinsun .
[566] [567] [568]
Underfull \hbox (badness 10000) in paragraph at lines 39087--39089
[]\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
[569] [570]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 39209--39209
 []\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 39211--39211
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[571] [572] [573] [574] [575]
Underfull \hbox (badness 6542) in paragraph at lines 39547--39549
[]\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
[576] [577]
Underfull \hbox (badness 1708) in paragraph at lines 39706--39714
[]\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 39706--39714
\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 10000) in paragraph at lines 39715--39719
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 39715--39719
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 39715--39719
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 39729--39734
[][][]\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;
[578] [579]
Underfull \hbox (badness 3895) in paragraph at lines 39791--39803
[]\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 39791--39803
\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 ,
[580] [581]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[582] [583]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 1803) in paragraph at lines 40650--40653
[]\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 ),
Underfull \hbox (badness 2334) in paragraph at lines 40654--40661
[]\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
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 40680--40684
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[592] [593] [594]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[595] [596] [597] [598]
Underfull \hbox (badness 6220) in paragraph at lines 41143--41148
[]\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,
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\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,
Underfull \hbox (badness 1533) in paragraph at lines 41143--41148
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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[]\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
[599]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[600]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
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\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
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[]\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
[601]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[602] [603] [604] [605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[607]
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[]\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
[608]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
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[]\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
[609]) (./compiler-pkg.tex [610]
Chapter 2.
[611] [612] [613]) (./datasets-pkg.tex [614]
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[615] [616] [617] [618] [619]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[620]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[621] [622] [623] [624] [625]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[626] [627]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[628] [629] [630] [631]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[632] [633] [634] [635] [636]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[637] [638]
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[]\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 ,
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\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
[639]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[640] [641]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[642]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[643] [644]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[645] [646] [647] [648]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[649] [650] [651] [652] [653] [654] [655] [656]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2674--2677
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[657]
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[658]
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[660]
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[661] [662]
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[663]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3091--3091
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[664] [665] [666] [667] [668] [669] [670]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3548--3548
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[671] [672]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[673]
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[674]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[675]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[676] [677] [678] [679] [680] [681] [682] [683] [684] [685]
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[687] [688]) (./grDevices-pkg.tex
Chapter 4.
[689] [690] [691] [692] [693] [694]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[695]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[696] [697] [698] [699] [700] [701] [702] [703] [704]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[705]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[706]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[707]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[708]
Underfull \hbox (badness 1173) in paragraph at lines 1268--1271
[]\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
[709] [710] [711]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[712]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[713] [714] [715]
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[]\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 1756--1761
\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
[716]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[717]
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[]\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 1880--1890
\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 ,
[718]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[719] [720]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[721] [722]
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\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
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\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
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\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
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\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
[723]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[724] [725] [726] [727] [728] [729]
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[730] [731] [732] [733] [734] [735]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[736] [737] [738] [739]
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 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[740]
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[]\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
[741]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[742] [743] [744] [745]
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[]\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 ,
[746] [747] [748] [749] [750]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[751] [752]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[753]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[754] [755]
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[756]
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[]\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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[757]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[758]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[759] [760]
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[]\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
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[][][]\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
[761] [762]
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\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 ,
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\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 ,
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\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 ),
[763]
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\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
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[]\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 /
[764] [765]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5154--5154
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[766]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 5352--5354
[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[769] [770] [771] [772] [773]
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 []\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 5724--5727
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[774] [775] [776] [777] [778] [779]
Underfull \hbox (badness 1189) in paragraph at lines 6121--6123
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[780] [781]
Underfull \hbox (badness 10000) in paragraph at lines 6219--6221
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\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
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\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[782]
Underfull \hbox (badness 3088) in paragraph at lines 6342--6346
[]\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
[783]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[784] [785]
Underfull \hbox (badness 5637) in paragraph at lines 6510--6516
\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 ,
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[]\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 /
[786] [787] [788]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
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[]\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
[789] [790] [791]) (./graphics-pkg.tex [792]
Chapter 5.
Underfull \hbox (badness 10000) 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
[793] [794] [795] [796]
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[]\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-
[797] [798] [799]
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\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
[800] [801] [802]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\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
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[][]\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
Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[803]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[804] [805]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[806] [807] [808] [809] [810] [811] [812]
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 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
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\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
[813]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[814]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
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 []\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 1431--1431
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[815] [816] [817] [818] [819]
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[][][]\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
[820]
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[821]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[822] [823]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[824] [825] [826] [827] [828]
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\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
[829] [830] [831] [832] [833]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[834] [835]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[836] [837]
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[][][]\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
[838] [839] [840]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[841]
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[]\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
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[842] [843] [844]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3388--3388
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[845]
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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[846] [847]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[848]
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 []                      \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 [849]
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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[850]
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[][][]\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
[851] [852]
Underfull \hbox (badness 1867) in paragraph at lines 3912--3916
[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[853] [854] [855]
Underfull \hbox (badness 3930) in paragraph at lines 4075--4077
[]\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
[856] [857] [858] [859]
Underfull \hbox (badness 1924) in paragraph at lines 4359--4364
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[860]
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\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
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[]\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
[861]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 
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 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[862]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[863]
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\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 ,
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[]\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.
[866]
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[870]
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[]\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
[871]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[872]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[873]
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[874] [875] [876]
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yramid" = 5),[] 
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[]\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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
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axis = "red")[] 
[882] [883] [884]
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 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
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[]\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
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[][] 
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[894]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[896]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[897]
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[]\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
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
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[902] [903] [904] [905] [906] [907]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[908]
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[909] [910] [911] [912] [913]
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us  =  FALSE,[] 
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us  =  FALSE,[] 
[914]
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[915] [916]
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[917] [918]
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[]\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
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lambda = 2),[] 
[921] [922]
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apse = ","),[] 
[923] [924]
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 []     \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�...")[] 
[925]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\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
[926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [927]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[928] [929]
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 []\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)[] 
[930]) (./grid-pkg.tex
Chapter 6.
[931] [932] [933] [934] [935] [936]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\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
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[]\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-
[948] [949] [950]
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[]\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
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[958] [959] [960]
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ck"), name="r1")[] 
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te"), name="r3")[] 
[961]
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[]\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 ,
[962]
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[]\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-
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[]\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
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[]\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
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FALSE)[] 
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[]\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-
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
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t(name="vp2"))))[] 
[981]
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[982]
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[]\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
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[984]
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[985] [986] [987]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[988] [989] [990] [991] [992] [993] [994] [995] [996]
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[]\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-
[997] [998] [999]
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[]\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
[1000]
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[]\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-
[1001] [1002] [1003]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012]
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[]\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
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
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\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1024] [1025] [1026] [1027] [1028]
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[]\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
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[][][]\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 ,
[1029] [1030]
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[]\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
[1031] [1032] [1033] [1034]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1035]) (./methods-pkg.tex [1036]
Chapter 7.
[1037] [1038] [1039]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1040] [1041] [1042] [1043] [1044] [1045]
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[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1046] [1047]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
Underfull \hbox (badness 3780) in paragraph at lines 851--857
\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 851--857
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058]
[1059] [1060]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1863--1863
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
Underfull \hbox (badness 10000) in paragraph at lines 1907--1909
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1061] [1062]
Underfull \hbox (badness 10000) in paragraph at lines 2050--2055
[]\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
[1063] [1064] [1065]
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("removeClass.msg", defaul
t=TRUE))[] 
[1066] [1067]
Underfull \hbox (badness 10000) in paragraph at lines 2409--2413
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1068] [1069] [1070]
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[]\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
[1071]
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[]\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
[1072]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1073] [1074]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1075]
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
[1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083]
Underfull \hbox (badness 10000) in paragraph at lines 3562--3566
[]\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
[1084]
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[]\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
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[]
[1085]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1086]
Underfull \hbox (badness 1394) in paragraph at lines 3835--3840
\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1087] [1088] [1089]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4097--4097
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1090] [1091] [1092]
Underfull \hbox (badness 10000) in paragraph at lines 4282--4284
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1093] [1094]
Underfull \hbox (badness 1629) in paragraph at lines 4384--4393
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1095]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4503--4503
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1096] [1097] [1098] [1099] [1100] [1101]
Underfull \hbox (badness 10000) in paragraph at lines 4975--4984
[]\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
[1102] [1103] [1104]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 5197--5197
 []\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 5211--5211
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
[1106]
Underfull \hbox (badness 1033) in paragraph at lines 5281--5288
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1107]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5357
[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1108] [1109] [1110] [1111]
Underfull \hbox (badness 1087) in paragraph at lines 5649--5654
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5662--5666
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5662--5666
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1112] [1113]
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1114] [1115]
Underfull \hbox (badness 10000) in paragraph at lines 5940--5956
[]\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
[1116] [1117] [1118]
Underfull \hbox (badness 1248) in paragraph at lines 6237--6241
[]\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 6237--6241
\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
[1119] [1120]
Underfull \hbox (badness 4647) in paragraph at lines 6392--6394
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
Underfull \hbox (badness 1072) in paragraph at lines 6469--6476
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1121] [1122] [1123]
Underfull \vbox (badness 10000) has occurred while \output is active [1124]
[1125]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6828 \aliasA{S4}{S3Part}{S4}
                               [1126] [1127] [1128]
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 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 
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 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
[1129]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7096 \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.7098 \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.7099 \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.7101 \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.7102 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\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
[1130]
Underfull \hbox (badness 6708) in paragraph at lines 7176--7188
[]\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 7176--7188
\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 7176--7188
\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 ,
[1131] [1132]
Underfull \hbox (badness 1694) in paragraph at lines 7336--7338
[]\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 7360--7363
[]\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
[1133] [1134] [1135] [1136] [1137] [1138]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7815--7815
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1139] [1140]
Underfull \hbox (badness 2277) in paragraph at lines 7950--7958
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing
[1141]
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[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
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[]\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
[1142] [1143] [1144] [1145] [1146]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8352--8352
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
Underfull \hbox (badness 1755) in paragraph at lines 8388--8391
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1147] [1148]
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 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1149] [1150] [1151] [1152] [1153]
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 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
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 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
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[1155]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1156] [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164]
Underfull \hbox (badness 10000) in paragraph at lines 9757--9759
[]\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
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[]\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 9765--9769
\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
[1165] [1166] [1167] [1168]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\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
[1169]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\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
[1170] [1171]
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[]\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
[1172]
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[]\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa
s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but
Underfull \hbox (badness 10000) in paragraph at lines 303--311
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1173] [1174]
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[]\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
[1175] [1176] [1177] [1178]
Underfull \hbox (badness 1917) in paragraph at lines 710--719
[]\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 710--719
\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
[1179] [1180]
Underfull \hbox (badness 10000) in paragraph at lines 847--850
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1181] [1182] [1183]
Underfull \hbox (badness 5388) in paragraph at lines 1036--1041
[]\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
[1184]
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[]\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
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 []\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)[] 
[1185] [1186]
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 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1254--1257
[]\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
[1187]
Underfull \hbox (badness 3375) in paragraph at lines 1300--1302
[]\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
[1188] [1189]) (./splines-pkg.tex [1190]
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
[1191] [1192] [1193] [1194] [1195] [1196] [1197]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1198] [1199] [1200] [1201]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 699--699
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1202] [1203] [1204]) (./stats-pkg.tex
Chapter 10.
[1205]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1206] [1207] [1208] [1209] [1210]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1024) in paragraph at lines 846--848
[]\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
[1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225]
Underfull \hbox (badness 10000) in paragraph at lines 1390--1392
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1226]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1506--1510
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
Underfull \hbox (badness 10000) in paragraph at lines 2079--2084
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
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\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2079--2084
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1236]
Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1237] [1238] [1239] [1240]
Underfull \hbox (badness 1221) in paragraph at lines 2431--2436
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2431--2436
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1241]
Underfull \hbox (badness 3965) in paragraph at lines 2508--2510
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1242] [1243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2643--2643
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1244] [1245] [1246] [1247]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2883--2883
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1248] [1249] [1250]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3076--3078
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1251]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3123--3123
 []\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 3124--3124
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1252] [1253] [1254] [1255] [1256]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3502--3502
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1257] [1258] [1259] [1260]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3772--3772
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1261] [1262] [1263] [1264] [1265]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4057--4057
 []\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 4058--4058
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1266] [1267] [1268] [1269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4293--4293
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1270] [1271]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4461--4461
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1272] [1273]
Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
[1274] [1275] [1276] [1277] [1278]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4913--4913
 []\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 4915--4915
 []\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))[] 
[1279]
Underfull \hbox (badness 7397) in paragraph at lines 5002--5006
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5002--5006
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1280] [1281]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5136--5136
 []\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 5154--5154
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1282]
Underfull \hbox (badness 2680) in paragraph at lines 5181--5183
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5186--5188
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1283] [1284] [1285]
Underfull \hbox (badness 1436) in paragraph at lines 5364--5369
[]\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 5364--5369
\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 5364--5369
\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 ,
[1286] [1287]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5550--5550
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1288]
Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1289] [1290]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5716--5716
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1291] [1292] [1293]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5901--5901
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1294] [1295] [1296]
Underfull \hbox (badness 10000) in paragraph at lines 6064--6069
[]\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
[1297] [1298] [1299]
Underfull \hbox (badness 5954) in paragraph at lines 6260--6262
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1300]
Underfull \hbox (badness 2503) in paragraph at lines 6342--6345
[]\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 6346--6348
[]\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 6349--6354
\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 6384--6387
[][][]\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
[1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6419--6419
 []\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 6434--6434
 []\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):[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6449--6449
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1303] [1304] [1305]
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 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1306] [1307] [1308] [1309] [1310] [1311]
Underfull \hbox (badness 10000) in paragraph at lines 7062--7066
\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
[1312]
Underfull \hbox (badness 6493) in paragraph at lines 7159--7162
[]\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
[1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320]
Underfull \hbox (badness 10000) in paragraph at lines 7706--7711
[]\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 , ...,
[1321] [1322]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7844--7846
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1323] [1324] [1325]
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[]\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
[1326] [1327] [1328] [1329] [1330] [1331] [1332]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8505--8505
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8527--8527
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8530--8530
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1333] [1334]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8668--8668
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1335]
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1336] [1337] [1338] [1339] [1340]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9060--9060
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1341] [1342]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1343] [1344] [1345] [1346] [1347] [1348] [1349]
Underfull \hbox (badness 2443) in paragraph at lines 9680--9686
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1350] [1351] [1352]
Underfull \hbox (badness 3758) in paragraph at lines 9894--9897
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1353] [1354] [1355] [1356]
Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1357]
Underfull \hbox (badness 4132) in paragraph at lines 10194--10198
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1358]
Underfull \hbox (badness 10000) in paragraph at lines 10297--10300
[]\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
[1359] [1360] [1361]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1362]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1363]
Underfull \hbox (badness 10000) in paragraph at lines 10620--10626
[][][]\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,
Underfull \hbox (badness 1418) in paragraph at lines 10658--10663
\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 (=
[1364] [1365]
Underfull \hbox (badness 2635) in paragraph at lines 10791--10794
\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
[1366] [1367] [1368]
Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
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[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
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\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1369]
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 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1370]
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 []            \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 11121--11125
[]\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
[1371] [1372] [1373]
Underfull \hbox (badness 7379) in paragraph at lines 11300--11303
[]\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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1374] [1375]
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 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1376]
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 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
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 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1377]
Underfull \hbox (badness 1062) in paragraph at lines 11566--11571
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1378] [1379]
Underfull \hbox (badness 3623) in paragraph at lines 11711--11713
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1380]
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 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1381] [1382]
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 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1383]
Underfull \hbox (badness 10000) in paragraph at lines 11940--11943
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1384] [1385] [1386]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
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[]\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
[1387]
Underfull \hbox (badness 2753) in paragraph at lines 12232--12234
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1388] [1389]
Underfull \hbox (badness 1292) in paragraph at lines 12357--12361
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1390] [1391]
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\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 12476--12480
\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
[1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1402] [1403] [1404]
Underfull \hbox (badness 10000) in paragraph at lines 13365--13369
[]\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
 ,
[1405] [1406] [1407]
Underfull \hbox (badness 6995) in paragraph at lines 13550--13552
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1408] [1409]
Underfull \hbox (badness 1163) in paragraph at lines 13698--13706
\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 ,
[1410] [1411]
Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1412] [1413]
Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 13956--13960
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1414]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14004--14004
 []\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 14005--14005
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1415]
Underfull \hbox (badness 10000) in paragraph at lines 14060--14063
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14060--14063
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1416] [1417] [1418] [1419]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14346--14346
 []\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 14347--14347
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1420]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14397--14399
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14440--14440
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1421] [1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 2726) in paragraph at lines 14843--14846
[]\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 ,
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15555--15555
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1439] [1440]
Underfull \hbox (badness 1648) in paragraph at lines 15746--15748
[]\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,
[1441]
Underfull \hbox (badness 2591) in paragraph at lines 15760--15769
\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 15760--15769
\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
[1442]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15824--15824
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450]
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 []\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[] 
[1451] [1452] [1453]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16605--16605
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1454] [1455] [1456] [1457] [1458] [1459] [1460]
Underfull \hbox (badness 2772) in paragraph at lines 17038--17041
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
Underfull \hbox (badness 10000) in paragraph at lines 17038--17041
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1461] [1462]
Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1463]
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Underfull \vbox (badness 10000) has occurred while \output is active [1465]
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 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1466]
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[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1467]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17490--17490
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17537--17537
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
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 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476]
Underfull \hbox (badness 1248) in paragraph at lines 18074--18077
[]\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 1127) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1477]
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\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
Underfull \hbox (badness 2042) in paragraph at lines 18148--18150
[]\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
[1478] [1479]
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 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
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 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
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 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1481]
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[]\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 18357--18368
\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
[1482]
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 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1483] [1484] [1485]
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 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1486]
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[]\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
[1487] [1488] [1489] [1490] [1491]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19027--19027
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1492] [1493]
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 []       \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]))),[] 
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 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1494] [1495] [1496] [1497] [1498]
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 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1499]
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[]\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
[1500]
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 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
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 []\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)[] 
[1501]
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
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\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1502]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19658--19658
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1503] [1504]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19780--19780
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1505]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1506]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1507]
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 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
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[1519] [1520]
Underfull \hbox (badness 6859) in paragraph at lines 20852--20859
[][][]\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 20863--20869
[]\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 ,
[1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]
[1532] [1533] [1534] [1535] [1536] [1537]
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 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1538] [1539] [1540] [1541] [1542]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
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Underfull \hbox (badness 1028) in paragraph at lines 22881--22884
[]\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
[1553] [1554]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22991--22994
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1555] [1556] [1557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23202--23202
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1558] [1559] [1560]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23422--23422
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1561] [1562]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\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
[1563]
Underfull \hbox (badness 2134) in paragraph at lines 23619--23623
[][][]\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
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 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1564] [1565] [1566] [1567] [1568] [1569] [1570]
Underfull \hbox (badness 2591) in paragraph at lines 24089--24095
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1571] [1572] [1573]
Underfull \hbox (badness 1867) in paragraph at lines 24286--24288
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1574]
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\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24333--24333
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1575] [1576] [1577]
Underfull \hbox (badness 2495) in paragraph at lines 24523--24532
[]\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 .
[1578]
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 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1579]
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 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1580]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 24757--24762
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1581] [1582]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24916--24916
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1583] [1584] [1585]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25086--25086
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1586]
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 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1587] [1588] [1589] [1590] [1591] [1592]
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 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1593] [1594]
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
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Underfull \hbox (badness 2922) in paragraph at lines 25775--25780
[]\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
[1596]
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[]\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
Underfull \hbox (badness 3240) in paragraph at lines 25849--25853
[][][]\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
[1597]
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[]\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
[1598]
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[]\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
[1599]
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 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
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 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1600] [1601]
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 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
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 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1602]
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[]\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
[1603]
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[]\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
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[]\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
[1604]
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[]\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
[1605]
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
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[]\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
[1606]
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 []\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 26433--26433
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1607] [1608] [1609] [1610] [1611] [1612] [1613]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1614] [1615] [1616] [1617] [1618] [1619] [1620]
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[]\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
[1621] [1622] [1623]
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[]\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
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[]\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
[1626]
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[]\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
[1627] [1628] [1629]
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[]\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)
[1630] [1631]
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[]\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
[1632] [1633]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1634] [1635]
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 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1636]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1637]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1638]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1639]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1640]
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[]\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
[1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29197--29197
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1649]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1650] [1651] [1652] [1653]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
Overfull \hbox (30.78088pt too wide) in paragraph at lines 29494--29494
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
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 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1654] [1655]
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 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
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 []\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:[] 
[1656] [1657] [1658] [1659]
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[]\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
[1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667]
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[]\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
[1668]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1669] [1670] [1671] [1672] [1673]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
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 []      \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[] 
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[]\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
[1674] [1675]
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1676]) (./stats4-pkg.tex
Chapter 11.
[1677] [1678] [1679]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1680] [1681] [1682]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}
                                                   [1683]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1684] [1685]) (./tcltk-pkg.tex [1686]
Chapter 12.
[1687] [1688] [1689] [1690]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1691] [1692] [1693]
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[]\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
[1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1706]) (./tools-pkg.tex
Chapter 13.
[1707]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1708]
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[]\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
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[]\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
[1709]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1710]
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[]\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
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\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-
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\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 ,
[1711]
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 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
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[]\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
[1712] [1713] [1714]
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[][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer /
 en / opentype /
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 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
[1721]
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1722]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\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-
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[]\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
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
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[]\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
[1726]
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[]\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
[1727]
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1728] [1729]
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 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
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 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
[1730]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1731] [1732] [1733]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.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1734]
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[]\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
[1735]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1736] [1737] [1738] [1739]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs
t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age
[1740]
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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
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[]\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-
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\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-
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\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
[1741]
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\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
[1742] [1743]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
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 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
[1744] [1745]
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 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
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[]\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
[1746] [1747] [1748] [1749] [1750] [1751]
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[]\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
[1752] [1753] [1754] [1755] [1756]
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 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1757] [1758] [1759]
Underfull \hbox (badness 4108) in paragraph at lines 3518--3525
[]\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
[1760] [1761]
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 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
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 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1762] [1763]
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[]\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
[1764] [1765] [1766] [1767]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\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 4037--4043
[]\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
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\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
[1768]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1769] [1770] [1771]
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 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
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\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 4294--4298
[]\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
[1772]
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[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1773] [1774]) (./utils-pkg.tex
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 ',
[1775] [1776] [1777]
Underfull \hbox (badness 1038) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1778]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1779] [1780] [1781]
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[]\T1/ptm/m/n/10 Kurt Hornik and Dun-can Mur-doch (2011), Watch your spelling! 
\T1/ptm/m/it/10 The R Jour-nal \T1/ptm/b/n/10 3\T1/ptm/m/n/10 (2),
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 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1782]
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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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[]\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 ,
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\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-
[1783] [1784]
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\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
[1785]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1786]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1787] [1788]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1789]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1790] [1791] [1792] [1793] [1794] [1795]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1796]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1797]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1798] [1799]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1800]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1801] [1802]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1803]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1804]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1805]
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[][][]\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;
[1806]
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[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2209--2216
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1807]
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[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1808] [1809] [1810]
Underfull \hbox (badness 10000) in paragraph at lines 2399--2401
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1811] [1812] [1813]
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1814]
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[]\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
[1815]
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 []\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 '[] 
[1816]
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[]\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
[1817] [1818] [1819] [1820] [1821] [1822]
Underfull \hbox (badness 1072) in paragraph at lines 3246--3254
[]\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
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[]\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
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\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
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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1823] [1824]
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\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
[1825] [1826] [1827]
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[]\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
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1828]
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 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1829] [1830] [1831] [1832] [1833]
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 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1834]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4109 ...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.4109 ...mat Unordered and Ordered Lists}{format}
                                                   [1835] [1836] [1837]
[1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848]
[1849]
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 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1850]
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[]\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
[1851]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1852] [1853]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\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
[1854]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
[1855] [1856]
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[]\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
[1857]
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1858]
Underfull \hbox (badness 5091) in paragraph at lines 5661--5663
[]\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
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 
[1859]
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[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
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\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 5807--5811
[]\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 1708) in paragraph at lines 5807--5811
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the ap-pro-pri-ate bi-nary type where
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[]\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-
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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1861]
Underfull \hbox (badness 1314) in paragraph at lines 5880--5887
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5901--5906
[][][]\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 ,
[1862]
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 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
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[]\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
[1863]
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 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1864]
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[]\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
[1865] [1866] [1867]
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 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1868] [1869]
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 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1870]
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[]\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
[1871] [1872]
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[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
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[]\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
[1873] [1874] [1875]
Underfull \hbox (badness 1859) in paragraph at lines 6808--6811
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1876]
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[]\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
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 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
[1877]
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 []\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):[] 
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 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1878] [1879] [1880] [1881]
Underfull \hbox (badness 10000) in paragraph at lines 7203--7205
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7208--7213
[]\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,
[1882] [1883]
Underfull \hbox (badness 10000) in paragraph at lines 7359--7364
[]\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
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[][]\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
[1884]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7369
[]\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
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[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1885]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1886] [1887] [1888] [1889]
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[]\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
[1890]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1891] [1892]
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1893]
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1894] [1895] [1896] [1897]
Underfull \hbox (badness 5203) in paragraph at lines 8319--8322
[]\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
[1898]
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[1900]
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[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1901]
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 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1902] [1903]
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 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1904] [1905]
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 []\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[] 
[1906] [1907]
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 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
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 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
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 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1908]
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[]\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
[1909] [1910] [1911] [1912] [1913] [1914]
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 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1915]
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[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1916] [1917]
Underfull \hbox (badness 2181) in paragraph at lines 9727--9731
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
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\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 9739--9743
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1918]
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 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1919] [1920]
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 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1921] [1922] [1923]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
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\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
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\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
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\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1924] [1925]
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[][][]$\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 /
[1926] [1927] [1928]
Underfull \hbox (badness 10000) in paragraph at lines 10447--10451
[]\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 10478--10484
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1929]
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1930]
Underfull \hbox (badness 2096) in paragraph at lines 10586--10588
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
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[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
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[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 10600--10603
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
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 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
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[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
[1931]
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[]\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
[1932]
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\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1933] [1934]
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1935]
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[]\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
[1936] [1937] [1938]
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[]\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-
[1939] [1940]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11322--11322
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1941]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
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\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1942]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 11405--11405
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1943] [1944]
Underfull \hbox (badness 10000) in paragraph at lines 11529--11531
[]\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
[1945] [1946]
Underfull \hbox (badness 4492) in paragraph at lines 11683--11690
[]\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 11683--11690
\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 2452) in paragraph at lines 11683--11690
\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$"\T1/ptm/m/n/10 ) and
[1947] [1948]
Underfull \hbox (badness 2020) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1949]
Underfull \hbox (badness 10000) in paragraph at lines 11930--11933
[][][]$\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 11930--11933
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957]
Underfull \hbox (badness 4467) in paragraph at lines 12427--12429
[]\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 12440--12444
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 12454--12458
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 3557) in paragraph at lines 12460--12462
[]\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 passed to
Underfull \hbox (badness 1052) in paragraph at lines 12463--12465
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1958]
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 12493--12498
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 12514--12519
[]\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 12522--12525
[][][]\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 ,
[1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 12764--12767
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12780--12780
 []\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:[]
 
[1963]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
Underfull \hbox (badness 1454) in paragraph at lines 12841--12845
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1964]
Underfull \hbox (badness 1715) in paragraph at lines 12866--12869
[]\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 12911--12913
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12923--12927
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1965] [1966] [1967]) [1968] [1969] [1970] (./KernSmooth-pkg.tex
Chapter 15.
[1971]
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) 
[1972] [1973] [1974] [1975] [1976]
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, 
[1977] [1978] [1979] [1980]) (./MASS-pkg.tex
Chapter 16.
[1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991]
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))[] 
[1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002]
[2003]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\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 2415--2415
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2015] [2016] [2017] [2018]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2019] [2020] [2021]
Underfull \hbox (badness 7362) in paragraph at lines 2863--2868
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/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/ptm/m/n/10 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2022] [2023]
Underfull \hbox (badness 4686) in paragraph at lines 3031--3033
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 3045--3049
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2024] [2025] [2026]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
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[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2027]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038]
[2039]
Underfull \hbox (badness 1845) in paragraph at lines 4162--4164
[]\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
[2040] [2041] [2042] [2043] [2044] [2045] [2046]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2047] [2048]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2049]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2050] [2051] [2052] [2053] [2054]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5292--5295
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2055]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2064]
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 []\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") 
[2065] [2066]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...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.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2067]
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[]\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
[2068] [2069] [2070] [2071]
Underfull \vbox (badness 10000) has occurred while \output is active [2072]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2073]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2074] [2075] [2076] [2077] [2078] [2079]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073
 []\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 7090--7090
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2080]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\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 ) =
[2081]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2082] [2083]
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\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
[2084] [2085]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2086]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2087] [2088] [2089] [2090] [2091] [2092]
Underfull \hbox (badness 4686) in paragraph at lines 7980--7982
[]\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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2093] [2094]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8123--8127
[]\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
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2115]
Underfull \hbox (badness 1158) in paragraph at lines 9629--9632
[]\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),
[2116]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128] [2129]) (./Matrix-pkg.tex [2130]
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
[2131]
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
[2132]
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
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\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
[2133]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\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
[2134] [2135]
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 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2136]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\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 534--534
 []\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 536--536
 []\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 545--545
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2137] [2138]
Underfull \hbox (badness 3189) in paragraph at lines 693--697
[]\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 .
[2139] [2140] [2141]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2142]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 1005--1010
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 1005--1010
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
[2143]
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2144]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1094 ...- '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.1094 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2145pdfTeX 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.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:pdfTeX warning (ext4): des
tination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has b
een already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:pdfTeX warning (ext4): des
tination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has b
een already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2146]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2147]
Underfull \hbox (badness 2277) in paragraph at lines 1348--1351
[]\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
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[]\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
[2148]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
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 []\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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2149]
Underfull \hbox (badness 6445) in paragraph at lines 1491--1498
[]\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 3861) in paragraph at lines 1491--1498
\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 1526--1530
[]\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
[2150]
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\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
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1583 ... 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.1583 ... 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.1584 \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.1605 \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.1616 \aliasA{rowSums}{colSums}{rowSums}
                                          [2151]
Underfull \hbox (badness 2922) in paragraph at lines 1670--1674
[]\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
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\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 1681--1684
[][][]\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
[2152]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2153]
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[]\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
[2154] [2155] [2156] [2157]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2158]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2255--2259
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2159]
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[]\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
[2160]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2161] [2162]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
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[]\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
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[]\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
[2163]
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[]\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 ;
Underfull \hbox (badness 2689) in paragraph at lines 2628--2630
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2164]
Underfull \hbox (badness 1097) in paragraph at lines 2654--2657
[]\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''
[2165]
Underfull \hbox (badness 3646) in paragraph at lines 2902--2905
[]\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
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[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\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
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[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2166]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
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[]\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 2963--2967
[][][]\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
[2167] [2168]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2169] [2170]
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[]\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
[2171]
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[]\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
[2172]
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2173] [2174]
Underfull \hbox (badness 10000) in paragraph at lines 3668--3673
[]\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
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\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 10000) in paragraph at lines 3678--3680
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2175]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
Underfull \hbox (badness 10000) in paragraph at lines 3791--3794
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 2318) in paragraph at lines 3791--3794
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2176]
Underfull \hbox (badness 6364) in paragraph at lines 3795--3798
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2177]
Underfull \hbox (badness 4060) in paragraph at lines 3915--3918
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2178]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3955--3955
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
Underfull \hbox (badness 3635) in paragraph at lines 4023--4027
[]\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
[2179]
Underfull \hbox (badness 10000) in paragraph at lines 4032--4035
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4032--4035
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4037--4041
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2180] [2181] [2182] [2183]
Underfull \hbox (badness 10000) in paragraph at lines 4325--4330
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2184] [2185]
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 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
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 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
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 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2186] [2187]
Underfull \hbox (badness 10000) in paragraph at lines 4631--4633
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2188] [2189]
Underfull \hbox (badness 10000) in paragraph at lines 4778--4783
[]\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 ,
[2190]
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 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
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 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
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 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
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 []  \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 '[] 
[2191] [2192]
Underfull \hbox (badness 4120) in paragraph at lines 5011--5014
[]\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
[2193]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5048--5048
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
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 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5060--5060
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
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 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2194]
Underfull \hbox (badness 1817) in paragraph at lines 5152--5161
[]\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 5637) in paragraph at lines 5194--5196
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2195]
Underfull \hbox (badness 3138) in paragraph at lines 5220--5222
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2196]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5284--5284
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5305--5307
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2197] [2198] [2199]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5542--5542
 []\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[] 
[2200]
Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[][][]\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 5634--5634
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2201]
Underfull \hbox (badness 1622) in paragraph at lines 5671--5676
[]\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 5671--5676
\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
[2202] [2203]
Underfull \hbox (badness 1062) in paragraph at lines 5857--5860
[]\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
[2204]
Underfull \hbox (badness 2809) in paragraph at lines 5886--5889
[]\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
[2205]
Underfull \hbox (badness 2635) in paragraph at lines 5998--6003
[]\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 5998--6003
\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 6006--6009
[]\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.,
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6127
\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 6117--6127
[][]\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
[2207]
Underfull \hbox (badness 1184) in paragraph at lines 6199--6202
[]\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
[2208]
Underfull \hbox (badness 10000) in paragraph at lines 6297--6300
[]\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.,
[2209]
Underfull \hbox (badness 10000) in paragraph at lines 6372--6375
[]\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 6388--6388
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2210]
Underfull \hbox (badness 2443) in paragraph at lines 6427--6433
[]\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 6427--6433
[][]\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 6448--6451
[]\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
[2211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6518--6518
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2212] [2213]
Underfull \hbox (badness 6268) in paragraph at lines 6654--6657
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2214]
Underfull \hbox (badness 5036) in paragraph at lines 6678--6682
[]\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 6678--6682
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2215]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6771 \aliasA{det}{Matrix-class}{det}
                                      
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[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6852--6855
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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Underfull \hbox (badness 7326) in paragraph at lines 6880--6882
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2216]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.6942 ...*\%}{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.7050 ...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.7150 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2217]
Underfull \hbox (badness 1881) in paragraph at lines 7248--7254
\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
[2218pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7310 \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.7310 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7320--7323
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7320--7323
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7323--7328
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7332--7334
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2219] [2220]
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[]\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
[2221]
Underfull \hbox (badness 2809) in paragraph at lines 7553--7556
[]\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
[2222]
Underfull \hbox (badness 10000) in paragraph at lines 7605--7607
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2223]
Underfull \hbox (badness 1406) in paragraph at lines 7645--7649
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7645--7649
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2224]
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
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Underfull \hbox (badness 2635) in paragraph at lines 7808--7813
[]\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 7808--7813
\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 7816--7819
[]\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.,
[2226] [2227]
Underfull \hbox (badness 10000) in paragraph at lines 8010--8012
[]\T1/ptm/m/n/10 fast
[2228]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8050 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
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<to be read again> 
                   \relax 
l.8050 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2229]
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[]\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 ,
[2230]
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[]\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
[2231]
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[]\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.,
[2232]
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[]\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 8484--8484
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2233] [2234]
Underfull \hbox (badness 10000) in paragraph at lines 8594--8596
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2235]
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2236]
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[]\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
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2237]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
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<to be read again> 
                   \relax 
l.8829 \aliasA{qr}{qr-methods}{qr}
                                   [2238]
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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 []                  \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)),[] 
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 []          \T1/pcr/m/n/9 all.equal(qr.coef(qxr, y), cf <- c(int=6, b1=-3, c1=
-2, c2=-1), tol=1e-15)[] 
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 []          \T1/pcr/m/n/9 all.equal(unname(qcfXy), unname(cf), tol=1e-15) || #
 FAIL names: ## FIXME_______[] 
[2239]
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 []          \T1/pcr/m/n/9 all.equal(unname(m(qcfXY)), unname(m(cf)), tol=1e-15
) || # FAIL dimnames: ## FIXME_______[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8936--8936
 []\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 (15.18042pt too wide) in paragraph at lines 8941--8941
 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co
rrect colnames[] 
[2240]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\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
[2241]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9079--9079
 []\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"[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9100--9100
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 
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 []\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.9116 ... the Reciprocal Condition Number}{rcond}
                                                   [2242] [2243]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9229--9229
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2244] [2245] [2246]
Underfull \hbox (badness 10000) in paragraph at lines 9412--9414
[]\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 1325) in paragraph at lines 9418--9426
\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2247] [2248]
Underfull \hbox (badness 1558) in paragraph at lines 9563--9566
[]\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
[2249]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9625--9625
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9691 \aliasA{solve}{solve-methods}{solve}
                                           
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9788--9788
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2251]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
Underfull \hbox (badness 2165) in paragraph at lines 9867--9877
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2252]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9960--9960
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2253]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\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,
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[]\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)
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\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
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\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
[2254]
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[]\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
[2255]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2256] [2257]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2258]
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[]\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
[2259]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2260]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\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)[] 
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 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
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 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
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 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2261]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
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[][][]\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
[2262]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10685 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2263]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2264]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10821--10821
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2265]
Underfull \hbox (badness 2970) in paragraph at lines 10974--10980
[]\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-
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\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 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2266]
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[]\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
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[]\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
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2267] [2268]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
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[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2269]
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[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
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[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
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[]\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
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\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
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\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
[2270]
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[]\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.,
[2271]
Underfull \hbox (badness 6641) in paragraph at lines 11457--11460
[]\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
[2272]
Underfull \hbox (badness 5133) in paragraph at lines 11497--11501
[]\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 11497--11501
\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
[2273]
Underfull \hbox (badness 7649) in paragraph at lines 11602--11604
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2274] [2275] [2276]
Underfull \hbox (badness 7362) in paragraph at lines 11797--11799
[]\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
[2277]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11835--11835
 []\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 11836--11836
 []\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)[] 
[2278] [2279]
Underfull \hbox (badness 6910) in paragraph at lines 12086--12088
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2280] [2281] [2282]) (./boot-pkg.tex
Chapter 18.
[2283] [2284] [2285] [2286] [2287] [2288] [2289]
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"), 
[2290]
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-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2291]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2292]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2293]
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 ,
[2294]
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 [2295]
[2296]
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
[2297]
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
[2298] [2299] [2300] [2301] [2302]
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-
[2303] [2304] [2305] [2306]
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), 
[2307] [2308] [2309] [2310]
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),[] 
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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.
[2312] [2313] [2314] [2315]
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
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.
[2316]
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 ,
[2317]
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
[2318] [2319] [2320] [2321] [2322]
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,[] 
[2323] [2324] [2325]
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 ,
[2326]
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)) 
[2327] [2328] [2329]
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 
[2330] [2331] [2332] [2333] [2334] [2335] [2336]
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)[] 
[2337] [2338]
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])[] 
[2339] [2340] [2341]
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
[2342]
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 
[2343] [2344]
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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2345] [2346] [2347] [2348] [2349] [2350] [2351] [2352] [2353]
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
[2354] [2355] [2356] [2357]
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
[2358]
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])[] 
[2359] [2360] [2361] [2362] [2363] [2364] [2365] [2366]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2367]
Underfull \hbox (badness 1127) in paragraph at lines 5984--6002
\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
[2368]
Underfull \hbox (badness 2837) in paragraph at lines 6017--6020
[]\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
[2369] [2370] [2371] [2372]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6302--6302
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2373] [2374]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6491--6491
 []\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 6493--6493
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2375] [2376] [2377]
Underfull \hbox (badness 1596) in paragraph at lines 6738--6742
[]\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
[2378] [2379]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6898--6898
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387]) (./class-pkg.tex
[2388]
Chapter 19.
[2389] [2390] [2391] [2392] [2393] [2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404]) (./cluster-pkg.tex
Chapter 20.
[2405]
Underfull \hbox (badness 3098) 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-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2406]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2407]
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]))[] 
[2408] [2409]
Underfull \vbox (badness 10000) has occurred while \output is active [2410]
[2411]
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,
 ...)[] 
[2412]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2413]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 636--636
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2414]
Underfull \hbox (badness 3078) in paragraph at lines 682--685
[]\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
[2415]
Underfull \hbox (badness 2941) in paragraph at lines 771--774
[][][]\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 
,
[2416]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 809--809
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 857--859
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
Overfull \hbox (90.78088pt too wide) in paragraph at lines 905--905
 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, d.power = 1, verbose =
 interactive(), ...) 
[2418]
Underfull \hbox (badness 4872) in paragraph at lines 952--954
[]\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 966--970
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2419] [2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1060--1060
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2421]
Underfull \hbox (badness 4144) in paragraph at lines 1136--1140
[]\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
[2422]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1212--1212
 []          \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 1218--1218
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2423] [2424]
Underfull \hbox (badness 10000) in paragraph at lines 1402--1405
[2425]
Underfull \hbox (badness 10000) in paragraph at lines 1419--1423
[][][]\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 1443--1443
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1452--1452
 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1460--1460
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2426]
Underfull \hbox (badness 5741) in paragraph at lines 1500--1503
[]\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
[2427] [2428]
Underfull \hbox (badness 5008) in paragraph at lines 1676--1684
\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
[2429]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1767--1767
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
[2430]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1786--1786
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2431] [2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 2088--2090
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
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Underfull \hbox (badness 3179) in paragraph at lines 2113--2119
[][][]\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.
[2435] [2436] [2437]
Underfull \hbox (badness 10000) in paragraph at lines 2271--2274
[][][]\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 ,
[2438]
Underfull \hbox (badness 1292) in paragraph at lines 2339--2342
[]\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 2348--2350
[]\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 2371--2374
[][][]\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 ,
[2439] [2440] [2441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2573--2573
 []\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 ):[] 
[2442] [2443] [2444]
Underfull \hbox (badness 1067) in paragraph at lines 2759--2764
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2814--2814
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2445] [2446]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2917--2917
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2447] [2448] [2449]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3113--3113
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3114--3114
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2450]
Underfull \hbox (badness 10000) in paragraph at lines 3181--3184
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2451]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3231--3231
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3232--3232
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2452] [2453] [2454]
Underfull \hbox (badness 10000) in paragraph at lines 3417--3420
[]\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
Underfull \hbox (badness 3471) in paragraph at lines 3417--3420
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2455]
Underfull \hbox (badness 10000) in paragraph at lines 3480--3485
[][][]\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 ,
[2456]
Underfull \hbox (badness 4621) in paragraph at lines 3542--3547
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3542--3547
\T1/ptm/m/n/10 which 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
Underfull \hbox (badness 6268) in paragraph at lines 3554--3557
[][][]\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 ,
[2457] [2458] [2459]
Underfull \hbox (badness 10000) in paragraph at lines 3739--3742
[][][]\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 3770--3773
[][][]\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 ,
[2460]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3823--3823
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
[2461]
Underfull \hbox (badness 2035) in paragraph at lines 3834--3836
[]\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
[2462] [2463] [2464]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4027--4027
 []     \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 4029--4029
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4058--4063
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 4125--4133
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2466]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4167--4167
 []\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 4176--4176
 []   \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 4178--4178
 []      \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 4181--4181
 []\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 4183--4183
 []   \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 4197--4197
 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474]) (./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,[] 
[2475]
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
[2476]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2477] [2478] [2479]) (./foreign-pkg.tex [2480]
Chapter 22.
[2481]
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
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2482] [2483]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2484]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2485] [2486] [2487]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 519--527
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2489]
Underfull \hbox (badness 7613) in paragraph at lines 537--543
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2490] [2491] [2492]
Underfull \hbox (badness 10000) in paragraph at lines 734--735
Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2493]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 820--820
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2494]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 884--884
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 910--913
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2495] [2496]
Underfull \hbox (badness 10000) in paragraph at lines 994--995
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1030--1030
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2497] [2498]
Underfull \hbox (badness 1286) in paragraph at lines 1115--1119
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2499]
Underfull \hbox (badness 10000) in paragraph at lines 1188--1194
[]\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 ,
[2500]) (./lattice-pkg.tex
Chapter 23.
[2501] [2502] [2503]
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"),[] 
[2504]
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"),[] 
[2505]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2506]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2507] [2508]
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
[2509] [2510] [2511] [2512]
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.
[2513]
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
[2514] [2515]
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
[2516] [2517] [2518]
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 ,
[2519]
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 ,
[2520]
Underfull \vbox (badness 10000) has occurred while \output is active [2521]
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
[2522]
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
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[]\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
[2523]
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
[2524] [2525] [2526]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2527]
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
[2528] [2529] [2530]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2531] [2532] [2533]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2534] [2535]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2536]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2537]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\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 2793--2798
\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 2879--2883
[]\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 2879--2883
\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 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2538]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\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 2937--2943
\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 2937--2943
\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 2961--2965
[]\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
[2539] [2540]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \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 3063--3063
 []      \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 3064--3064
 []      \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 3075--3075
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2541]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\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 3145--3152
\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
[2542] [2543] [2544] [2545]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2546]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2547] [2548] [2549] [2550] [2551]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2552]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2553] [2554]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\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 4090--4092
[]\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 4107--4111
\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
[2555]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\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 4172--4176
\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
[2556] [2557]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\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 4286--4296
\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 4286--4296
\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 4286--4296
\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 4286--4296
\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 4311--4314
[]\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 4314--4316
[]\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
[2558] [2559] [2560] [2561] [2562] [2563]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2564] [2565]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\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 .
[2566] [2567]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\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
[2568] [2569] [2570] [2571] [2572] [2573]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\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 5399--5399
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2574]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\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 5488--5491
\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
Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2575]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\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
[2576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2577]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2578]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2579]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\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 5859--5866
[]\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 5859--5866
\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
[2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\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 ,
[2582] [2583]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2584] [2585]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\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 6275--6280
\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
[2586] [2587]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2588]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\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
[2589]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\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 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2590]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2591] [2592] [2593] [2594] [2595]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\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 6957--6964
\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
[2596]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2597]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\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 7057--7060
\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
[2598]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\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
[2599] [2600]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2601]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2602] [2603]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\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 7527--7530
[]\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
Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
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\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
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\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2604]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2605]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2606] [2607] [2608]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2609]
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[]\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
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\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\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
[2618] [2619]
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2620]
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[]\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
[2621]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2622]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2623] [2624]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2625] [2626]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2627]
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[]\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
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\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
[2628] [2629] [2630] [2631] [2632] [2633] [2634]
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[]\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 ,
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\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 ,
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[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2635] [2636] [2637]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2638] [2639] [2640] [2641])
(./mgcv-pkg.tex [2642]
Chapter 24.
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[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2643] [2644]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
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 []    \T1/pcr/m/n/10 sparse=FALSE,cluster=NULL,nthreads=NA,gc.level=1,use.chol
=FALSE,[] 
[2645]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2646] [2647] [2648] [2649]
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[][][]\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 ,
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[][]\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 ,
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[][]\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 ,
[2650] [2651] [2652] [2653]
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[]\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
[2654]
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[]\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
[2655] [2656] [2657] [2658] [2659] [2660] [2661]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2662]
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 []\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)[] 
[2663] [2664] [2665] [2666] [2667] [2668]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2669] [2670] [2671] [2672] [2673] [2674]
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\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
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
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 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 
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[]\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
[2675]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2676] [2677] [2678]
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\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
[2679]
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[][][]\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 ,
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[][]\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 ,
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[][]\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 ,
[2680] [2681]
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[2684] [2685] [2686] [2687] [2688] [2689] [2690]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2691] [2692] [2693] [2694] [2695]
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[]\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
[2696]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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[2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706]
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 []  \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)+[] 
[2707] [2708]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2709] [2710] [2711]
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[][][]\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 ,
[2712]
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[]\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
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
[2725]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2726] [2727] [2728]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
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[2766]
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[]\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 7497--7500
\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 ,
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\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 .
[2767]
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[]\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 ,
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\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
[2768] [2769] [2770]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 
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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
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\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
[2774] [2775] [2776]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2777] [2778] [2779] [2780] [2781] [2782]
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 []  \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[] 
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Underfull \hbox (badness 1205) in paragraph at lines 8571--8573
[]\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 8571--8573
\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 8577--8582
[]\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
[2784]
Underfull \hbox (badness 1205) in paragraph at lines 8661--8663
[]\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 8661--8663
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2785]
Underfull \hbox (badness 10000) in paragraph at lines 8730--8733
[]\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 8730--8733
[][]\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,
[2786] [2787] [2788]
Underfull \hbox (badness 1253) in paragraph at lines 8860--8862
[]\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,
[2789] [2790] [2791]
Underfull \hbox (badness 1946) in paragraph at lines 9038--9045
[]\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 9038--9045
\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 9038--9045
\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 9046--9049
[]\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 9046--9049
\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.
[2792]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 9089--9089
 []\T1/pcr/m/n/9 ## see also examples for gam.models, gam.vcomp, gamm and smoot
h.construct.re.smooth.spec 
[2793]
Underfull \hbox (badness 10000) in paragraph at lines 9125--9128
[]\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 ,
[2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] [2803] [2804]
[2805]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9823--9823
 [] \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 9834--9839
[]\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
[2806]
Underfull \hbox (badness 1803) in paragraph at lines 9911--9915
\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 9923--9935
\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
[2807]
Underfull \hbox (badness 2401) in paragraph at lines 9940--9944
\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 9940--9944
\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 ,
[2808] [2809]
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Underfull \hbox (badness 6876) in paragraph at lines 10135--10141
[][][]\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
[2811]
Underfull \hbox (badness 10000) in paragraph at lines 10176--10177
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2812] [2813]
Underfull \hbox (badness 10000) in paragraph at lines 10294--10295
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2814]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10355--10355
 []  \T1/pcr/m/n/9 sm <- smoothCon(s(x,bs="bs",m=m,k=k),data.frame(x),scale.pen
alty=FALSE)[[1]][] 
Underfull \hbox (badness 10000) in paragraph at lines 10399--10401
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
Underfull \hbox (badness 10000) in paragraph at lines 10399--10401
\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
[2815] [2816] [2817]
Underfull \hbox (badness 10000) in paragraph at lines 10527--10528
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2818]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10608--10608
 []\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 10609--10609
 []\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[] 
[2819]
Underfull \hbox (badness 7613) in paragraph at lines 10647--10650
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2820] [2821]
Underfull \hbox (badness 10000) in paragraph at lines 10756--10757
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2822] [2823] [2824] [2825]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10993--10993
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 11038--11040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2826] [2827]
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Underfull \hbox (badness 10000) in paragraph at lines 11197--11200
[]\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 11197--11200
\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 11197--11200
\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"
[2829] [2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11279--11279
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
Underfull \hbox (badness 10000) in paragraph at lines 11324--11330
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 11324--11330
\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-
[2831] [2832] [2833]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 11538--11538
 []\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...[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 11540--11540
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 11541--11541
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 
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Overfull \hbox (90.78033pt too wide) in paragraph at lines 11622--11622
 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 
Overfull \hbox (85.38034pt too wide) in paragraph at lines 11628--11628
 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2836]
Underfull \hbox (badness 10000) in paragraph at lines 11642--11650
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 11668--11669
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2837] [2838] [2839] [2840]
Underfull \hbox (badness 3396) in paragraph at lines 11929--11934
[][][]\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
[2841]
Underfull \hbox (badness 10000) in paragraph at lines 11974--11976
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2842] [2843] [2844] [2845]
Underfull \hbox (badness 10000) in paragraph at lines 12170--12173
[]\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 12170--12173
\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
Underfull \hbox (badness 10000) in paragraph at lines 12203--12207
[][][]\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 12203--12207
[][]\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 12203--12207
[][]\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 ,
[2846] [2847] [2848]
Underfull \hbox (badness 2158) in paragraph at lines 12363--12363
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2849]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 12438--12438
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2850] [2851]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 12572--12572
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2852] [2853] [2854]
Underfull \hbox (badness 4846) in paragraph at lines 12708--12711
[]\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
[2855] [2856] [2857] [2858] [2859]
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[2861] [2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 13678--13678
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2870] [2871] [2872] [2873] [2874]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 13968--13968
 []\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 13969--13969
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
[2875]
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 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2876] [2877]) (./nlme-pkg.tex [2878]
Chapter 25.
[2879]
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
[2880]
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
[2881] [2882] [2883] [2884] [2885]
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,[] 
[2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895]
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 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[2896]
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
[2897] [2898] [2899] [2900] [2901] [2902] [2903]
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 ,
[2904]
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
[2905] [2906] [2907] [2908] [2909]
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 ,
[2910]
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")[] 
[2911]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2912] [2913]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[2914]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2915] [2916] [2917] [2918] [2919] [2920] [2921] [2922]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933]
[2934]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4345--4345
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2946] [2947] [2948] [2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956]
[2957] [2958]
Underfull \hbox (badness 10000) in paragraph at lines 5155--5159
[][][]\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 ,
[2959] [2960] [2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 5472--5476
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5472--5476
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2964] [2965]
Underfull \hbox (badness 10000) in paragraph at lines 5587--5590
[][][]\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 ,
[2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
Underfull \hbox (badness 2799) in paragraph at lines 6093--6099
\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
[2975]
Underfull \hbox (badness 7133) in paragraph at lines 6154--6158
[]\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 ,
[2976]
Underfull \hbox (badness 2057) in paragraph at lines 6238--6249
[][][]\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 ,
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6306
[]\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 6336--6336
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2978] [2979] [2980] [2981]
Underfull \hbox (badness 7133) in paragraph at lines 6554--6558
[]\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 ,
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 6653--6659
[][][]\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 ,
[2983]
Underfull \hbox (badness 10000) in paragraph at lines 6719--6721
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2984]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6749--6749
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2985] [2986] [2987]
Underfull \hbox (badness 10000) in paragraph at lines 6992--6999
[][][]\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 ,
[2988]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7009--7009
 []                \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
[2989] [2990] [2991]
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 ,
[2992] [2993] [2994]
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 1817) 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 
20 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 ,
[2995] [2996] [2997]
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
[2998] [2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 1642) in paragraph at lines 8036--8058
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3004] [3005]
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
[3006] [3007] [3008] [3009] [3010]
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 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3011]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3012] [3013] [3014]
Underfull \hbox (badness 10000) in paragraph at lines 8722--8734
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9320
[][][]\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 9324--9324
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3024]
Underfull \hbox (badness 6300) in paragraph at lines 9406--9409
[]\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
[3025] [3026] [3027] [3028]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9675 ...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.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3029]
Underfull \hbox (badness 10000) in paragraph at lines 9695--9698
[]\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 9739--9742
[]\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 9739--9742
\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
[3030] [3031] [3032]
Underfull \hbox (badness 2435) in paragraph at lines 9913--9918
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 7291) in paragraph at lines 10203--10205
[]\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
[3038] [3039] [3040]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3041]
Underfull \hbox (badness 1596) in paragraph at lines 10448--10474
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3042] [3043] [3044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3045] [3046]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
[3047]
Underfull \hbox (badness 10000) in paragraph at lines 10823--10825
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10835--10838
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10858--10858
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060] [3061] [3062]
Underfull \hbox (badness 6268) in paragraph at lines 11890--11900
[][][]\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 ,
[3063] [3064] [3065] [3066]
Underfull \hbox (badness 10000) in paragraph at lines 12151--12157
[][][]\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 ,
[3067] [3068] [3069] [3070] [3071]
Underfull \hbox (badness 6876) in paragraph at lines 12473--12475
[]\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
[3072] [3073]
Underfull \hbox (badness 2452) in paragraph at lines 12629--12636
[][][]\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 ,
[3074]
Underfull \hbox (badness 10000) in paragraph at lines 12694--12700
[][][]\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 ,
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
[3086] [3087] [3088] [3089]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13646--13646
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
Underfull \hbox (badness 10000) in paragraph at lines 13673--13676
[]\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
[3090]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13701--13704
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13708--13711
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13716--13723
[]\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 13716--13723
\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
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13773--13773
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13780--13783
[]\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 13780--13783
\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
[3092]
Underfull \hbox (badness 4582) in paragraph at lines 13808--13811
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13808--13811
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13812--13815
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3093]
Underfull \hbox (badness 10000) in paragraph at lines 13888--13891
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13913--13920
\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 ,
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 13982--13984
[][][]\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 ,
[3095] [3096] [3097]
Underfull \hbox (badness 1540) in paragraph at lines 14197--14202
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
[3098]
Underfull \hbox (badness 1215) in paragraph at lines 14244--14246
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3099] [3100] [3101] [3102] [3103]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14488--14488
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]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.15144 ...Extract Random Effects}{random.effects}
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ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
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                   \relax 
l.15144 ...Extract Random Effects}{random.effects}
                                                   [3113] [3114] [3115]
[3116] [3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1009) in paragraph at lines 15801--15810
\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
[3123] [3124] [3125]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15948--15948
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3126] [3127] [3128] [3129]
Underfull \hbox (badness 10000) in paragraph at lines 16226--16244
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16226--16244
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3130]
Underfull \hbox (badness 10000) in paragraph at lines 16283--16289
[][][]\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 ,
[3131]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16314--16314
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3132] [3133] [3134] [3135] [3136] [3137] [3138]
Underfull \hbox (badness 1728) in paragraph at lines 16798--16801
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3139] [3140] [3141] [3142] [3143]
Underfull \hbox (badness 1867) in paragraph at lines 17131--17140
\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 17131--17140
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3144]
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\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 ,
[3145] [3146] [3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 17442--17449
[][][]\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 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156]
Underfull \hbox (badness 10000) in paragraph at lines 17972--17982
[][][]\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 17972--17982
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18010--18015
\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
[3157]
Underfull \hbox (badness 3579) in paragraph at lines 18074--18079
\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
[3158]
Underfull \hbox (badness 3579) in paragraph at lines 18137--18142
\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
[3159]
Underfull \hbox (badness 1577) in paragraph at lines 18198--18200
[]\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 18200--18205
\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
[3160]
Underfull \hbox (badness 3579) in paragraph at lines 18263--18268
\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
[3161]
Underfull \hbox (badness 10000) in paragraph at lines 18296--18305
[][][]\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 18296--18305
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18335--18340
\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
[3162] [3163] [3164]
Underfull \hbox (badness 1009) in paragraph at lines 18484--18493
\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
[3165] [3166]
Underfull \hbox (badness 1009) in paragraph at lines 18618--18627
\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
[3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174]) (./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}
                                                   [3175]
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,[] 
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3176] [3177] [3178]
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,[] 
[3179]
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)[] 
[3180]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3181]
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,[] 
[3182]) (./rpart-pkg.tex
Chapter 27.
[3183] [3184] [3185] [3186]
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, ...)[] 
[3187]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3188] [3189] [3190]
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
[3191] [3192]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3193]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3194]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3195]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3196] [3197] [3198]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3199]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3200]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\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 1286--1286
 []\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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3201] [3202] [3203] [3204] [3205] [3206]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3207] [3208]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3209] [3210] [3211]) (./spatial-pkg.tex [3212]
Chapter 28.
[3213] [3214] [3215] [3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3219] [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
[3230] [3231]) (./survival-pkg.tex [3232]
Chapter 29.
[3233] [3234]
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[] 
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 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
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 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3235]
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 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... 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.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3236] [3237]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
 []\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 366--366
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3238]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3239] [3240] [3241]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 598--598
 []\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 599--599
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3242] [3243]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 742--742
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3244] [3245] [3246]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 972--972
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3247]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1040 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3248] [3249] [3250]
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1854--1854
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3259] [3260] [3261] [3262]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2101--2101
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3263] [3264] [3265] [3266]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2418--2418
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3267]
Underfull \hbox (badness 1389) in paragraph at lines 2431--2433
[]\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
Underfull \hbox (badness 1048) in paragraph at lines 2474--2476
[]\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
[3268]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2545--2545
 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2551--2551
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3269] [3270] [3271] [3272] [3273]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2798--2798
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3274] [3275] [3276]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3027--3027
 []                    \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 )))[] 
[3277] [3278] [3279] [3280]
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[3282] [3283]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3436--3436
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3284] [3285]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3625--3625
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3286] [3287]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3739--3739
 []\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[] 
[3288]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3289] [3290] [3291]
Underfull \hbox (badness 1852) in paragraph at lines 3977--3979
[]\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
[3292] [3293]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4110--4110
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3294] [3295]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3296]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3297]
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 []\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 4394--4394
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3298] [3299]
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 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3300] [3301] [3302] [3303]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
[3304]
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3305] [3306]
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 []\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 5053--5053
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
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 []    \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 ),[] 
[3314] [3315] [3316] [3317]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3318]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3319]
Underfull \hbox (badness 1038) in paragraph at lines 5969--5975
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3320]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3321]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3322] [3323] [3324]
Underfull \hbox (badness 10000) in paragraph at lines 6314--6319
[][][]\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 ,
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3325] [3326]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3327] [3328]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3329] [3330]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3331] [3332] [3333]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3334]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3335] [3336]
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\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 .
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\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 7293--7300
\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
[3337]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3338] [3339] [3340]
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 []                 \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 )[] 
[3341] [3342]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \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 )[] 
[3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3347] [3348] [3349] [3350] [3351]) [3352] (./fullrefman.ind [3353] [3354]
[3355] [3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365]
[3366] [3367] [3368] [3369] [3370] [3371] [3372]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
[3373]
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3374] [3375] [3376] [3377] [3378]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3379]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,missing,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,TsparseMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,TsparseMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,TsparseMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,denseMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,missing-method 
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[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,sparseMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,sparseMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method 
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[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method 
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[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method 
[3388]
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,sparseVector-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,lsparseMatrix,missing,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,matrix,missing,replValue-method 
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,replValue-method 
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[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method 
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[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,matrix-method 
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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4]
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Chapter 1.
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
char-ac-ter vec-tors. The first en-try is al-ways
[4]
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[]\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
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\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base 
^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \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,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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[]\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 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if
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\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6] [7]
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[][][]\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]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
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[]\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]
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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19]
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[]\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
[20] [21] [22] [23]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
 of
[27]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[28]
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[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then
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[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[29] [30]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())
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[]\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]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[35] [36]
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[]\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
[37] [38] [39] [40] [41]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[56] [57] [58] [59] [60] [61]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\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
[62] [63] [64]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[65] [66]
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 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[67]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
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\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[68]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[69] [70] [71] [72]
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[]\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
[73] [74] [75] [76] [77] [78]
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[]\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
[79] [80] [81] [82] [83] [84] [85] [86]
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[]\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 : / /
[87] [88] [89]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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 []\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}[] 
[90] [91]
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[]\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
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[]\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
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\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
[92] [93]
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[94]
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[]\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 : 
[95] [96]
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[]\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
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\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
[97] [98]
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\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[99]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[100] [101]
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 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[103] [104] [105] [106]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[107] [108]
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 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[109]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[110] [111] [112]
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 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[113] [114]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
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\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
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[]\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 1062) in paragraph at lines 7671--7682
[][]\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
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[]\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")
[115] [116] [117] [118] [119] [120]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[121] [122] [123]
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[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[124] [125]
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\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
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[]\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
[126] [127]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[128] [129]
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[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[130]
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\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[131] [132]
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[]\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
[133] [134] [135] [136] [137] [138] [139] [140]
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[]\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
[141]
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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
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 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[142] [143]
Underfull \hbox (badness 1168) in paragraph at lines 9698--9703
\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
[144] [145]
Underfull \hbox (badness 2828) in paragraph at lines 9836--9840
[][][]$\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 9836--9840
\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 _
[146] [147] [148]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10067--10067
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[149]
Underfull \hbox (badness 1629) in paragraph at lines 10141--10145
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[150] [151]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 10254--10262
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10263--10265
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[152]
Underfull \hbox (badness 3735) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[153] [154]
Underfull \hbox (badness 10000) in paragraph at lines 10490--10493
[]\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
[155] [156] [157] [158] [159] [160] [161] [162] [163]
Underfull \hbox (badness 5288) in paragraph at lines 11156--11158
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 11166--11171
[]\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
[164]
Underfull \hbox (badness 10000) in paragraph at lines 11224--11226
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[165] [166]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\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 11341--11345
\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
[167] [168]
Underfull \hbox (badness 10000) in paragraph at lines 11456--11458
[]\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
Underfull \hbox (badness 2790) in paragraph at lines 11499--11501
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[169] [170] [171]
Underfull \hbox (badness 4048) in paragraph at lines 11669--11679
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 11669--11679
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[172] [173] [174]
Underfull \hbox (badness 5460) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[175] [176] [177] [178] [179]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 12280--12280
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[180] [181] [182] [183]
Underfull \hbox (badness 5119) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[184] [185]
Underfull \hbox (badness 2221) in paragraph at lines 12703--12709
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[186] [187] [188]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[189] [190]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[191] [192]
Underfull \hbox (badness 10000) in paragraph at lines 13205--13207
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[193] [194]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\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 (30.78088pt too wide) in paragraph at lines 13355--13355
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[195] [196]
Underfull \hbox (badness 10000) in paragraph at lines 13447--13450
[][][]\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 (4.38043pt too wide) in paragraph at lines 13457--13457
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[197]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13545--13545
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 7238) in paragraph at lines 13569--13576
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 13569--13576
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 13569--13576
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
[198] [199] [200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13740--13740
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13741--13741
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[201] [202]
Underfull \hbox (badness 10000) in paragraph at lines 13820--13824
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 13820--13824
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[203] [204]
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 []\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 13971--13971
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[205]
Underfull \hbox (badness 1168) in paragraph at lines 14055--14059
[]\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 14055--14059
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[206]
Underfull \hbox (badness 6944) in paragraph at lines 14149--14152
[][][]\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 ,
[207]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14174--14174
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[208] [209]
Underfull \hbox (badness 10000) in paragraph at lines 14308--14310
[]\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 14327--14327
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14329--14329
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14332--14332
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
Underfull \hbox (badness 2790) in paragraph at lines 14338--14341
[]\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 4254) in paragraph at lines 14354--14362
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14369--14373
[]\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
[210]
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[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\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,
Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14441--14449
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[212]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14545--14545
 []\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 ")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [213]
[214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225]
[226]
Underfull \hbox (badness 2418) in paragraph at lines 15479--15483
\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 15486--15489
[]\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 15514--15521
[][][]\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 ,
[227] [228] [229] [230]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[231] [232] [233] [234]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16024--16024
 []  \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 16053--16053
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [235]
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 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 16110--16114
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16110--16114
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[236] [237] [238] [239]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16453--16453
 []\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))) 
[240] [241] [242] [243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16703--16703
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[244] [245] [246] [247]
Underfull \hbox (badness 2435) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
Underfull \hbox (badness 1867) in paragraph at lines 17006--17013
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17006--17013
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
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\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
[248]
Underfull \hbox (badness 2285) in paragraph at lines 17021--17023
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17029--17029
 []\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.[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17039--17039
 []    \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 17059--17059
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[249] [250] [251] [252] [253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17520--17522
[]\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
[256]
Underfull \hbox (badness 4217) in paragraph at lines 17604--17613
[][][]\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 17619--17635
[][][]\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 ,
[257] [258] [259] [260] [261] [262]
Underfull \hbox (badness 4699) in paragraph at lines 18033--18036
[]\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 ,
[263] [264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18158--18158
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[265] [266]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[267] [268] [269] [270] [271] [272]
Underfull \hbox (badness 1430) in paragraph at lines 18700--18705
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 18700--18705
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[273]
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 18761--18766
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 18761--18766
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[274]
Underfull \hbox (badness 10000) in paragraph at lines 18821--18828
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 18821--18828
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 18821--18828
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
Underfull \hbox (badness 5908) in paragraph at lines 18821--18828
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 18837--18839
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[275] [276]
Underfull \hbox (badness 1975) in paragraph at lines 18909--18912
[]\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
[277] [278] [279] [280] [281]
Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\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
[283] [284]
Underfull \hbox (badness 10000) in paragraph at lines 19475--19479
[]\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 19475--19479
[][]\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
[285]
Underfull \hbox (badness 10000) in paragraph at lines 19571--19578
[][][]\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 ,
[286] [287]
Underfull \hbox (badness 10000) in paragraph at lines 19692--19696
[]\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
[288]
Underfull \hbox (badness 5161) in paragraph at lines 19747--19752
[]\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 19747--19752
\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 19747--19752
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 19747--19752
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[289] [290] [291]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19913--19913
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19917--19917
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Underfull \hbox (badness 3343) in paragraph at lines 19973--19977
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[292] [293]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20059--20059
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20070--20070
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[294] [295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20180--20180
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (85.38034pt too wide) in paragraph at lines 20183--20183
 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects
 w/ same name in .GlobalEnv[] 
Underfull \hbox (badness 6380) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[296]
Underfull \hbox (badness 10000) in paragraph at lines 20256--20259
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1337) in paragraph at lines 20285--20292
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 2229) in paragraph at lines 20285--20292
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
Underfull \hbox (badness 1043) in paragraph at lines 20285--20292
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
Underfull \hbox (badness 2564) in paragraph at lines 20304--20307
[]\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
[297]
Underfull \hbox (badness 1205) in paragraph at lines 20357--20362
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[298] [299] [300] [301]
Underfull \hbox (badness 2469) in paragraph at lines 20667--20673
[]\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 1939) in paragraph at lines 20667--20673
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 20667--20673
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[302] [303] [304] [305] [306]
Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 1655) in paragraph at lines 21382--21386
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[313] [314] [315] [316]
Underfull \hbox (badness 2277) in paragraph at lines 21628--21631
[]\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.
[317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 10000) in paragraph at lines 22108--22114
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22108--22114
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
[]\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 2951) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22140--22148
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[324] [325]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22217--22217
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[326]
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 22268--22272
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[327] [328] [329] [330] [331] [332]
Underfull \hbox (badness 10000) in paragraph at lines 22707--22715
\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 ;
[333]
Underfull \hbox (badness 3849) in paragraph at lines 22821--22826
[]\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
[334]
Underfull \hbox (badness 7308) in paragraph at lines 22898--22904
[]\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 5077) in paragraph at lines 22898--22904
\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 10000) in paragraph at lines 22908--22911
[]\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 22908--22911
\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
[335] [336] [337]
Underfull \hbox (badness 10000) in paragraph at lines 23060--23062
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[338] [339] [340] [341] [342] [343] [344] [345] [346]
Underfull \hbox (badness 2197) in paragraph at lines 23722--23726
[]\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 23722--23726
\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
[347]
Underfull \hbox (badness 2846) in paragraph at lines 23736--23740
[]\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 23736--23740
\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
[348]
Underfull \hbox (badness 10000) in paragraph at lines 23826--23832
[]\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 23826--23832
\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 23839--23841
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[349]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 23890--23890
 [] \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:[] 
[350] [351]
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[352] [353]
Underfull \hbox (badness 4120) in paragraph at lines 24152--24159
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[354]
Underfull \hbox (badness 1694) in paragraph at lines 24288--24291
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[355] [356] [357] [358]
Underfull \hbox (badness 1603) in paragraph at lines 24527--24529
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[359]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 24645--24653
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[360]
Underfull \hbox (badness 5475) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[361]
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[362]
Overfull \vbox (2.42159pt too high) has occurred while \output is active
[363]
Underfull \hbox (badness 3138) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[364]
Underfull \hbox (badness 1194) in paragraph at lines 25047--25050
[]\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 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25083--25087
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25088--25094
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25109--25120
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25121--25124
[]\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
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
[]\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 25145--25152
[]\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 10000) in paragraph at lines 25145--25152
\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
Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 25145--25152
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[366] [367] [368] [369]
Underfull \vbox (badness 10000) has occurred while \output is active [370]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25478--25478
 []\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 25491--25495
[]\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 25491--25495
\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)]
[371] [372] [373] [374]
Underfull \hbox (badness 4341) in paragraph at lines 25814--25816
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[375]
Underfull \hbox (badness 4518) in paragraph at lines 25850--25856
[][][]\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
Overfull \hbox (42.18039pt too wide) in paragraph at lines 25872--25872
 []\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 25884--25884
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[376] [377] [378] [379] [380] [381] [382]
Underfull \hbox (badness 10000) in paragraph at lines 26306--26310
[]\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,
[383]
Underfull \hbox (badness 1796) in paragraph at lines 26369--26372
[]\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
[384] [385] [386]
Underfull \hbox (badness 10000) in paragraph at lines 26564--26567
[]\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
[387] [388] [389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 1226) in paragraph at lines 27186--27191
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[396]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27231--27231
 []           \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))[] 
[397] [398] [399] [400]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27497--27497
 []\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 27508--27508
 []\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 27514--27514
 []\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 27515--27515
 []\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 27518--27518
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[401]
Underfull \hbox (badness 7415) in paragraph at lines 27593--27597
[]\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
[402]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27614--27614
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[403]
Underfull \hbox (badness 2418) in paragraph at lines 27762--27773
[]\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
[404] [405]
Underfull \hbox (badness 1248) in paragraph at lines 27886--27893
\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 27886--27893
\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 /
[406]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[407] [408]
Underfull \hbox (badness 1337) in paragraph at lines 28092--28095
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[409]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 28140--28140
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 28157--28168
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 28169--28172
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[410] [411]
Underfull \hbox (badness 1117) in paragraph at lines 28264--28270
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 4048) in paragraph at lines 28639--28644
[]\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 28639--28644
\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 28639--28644
\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 ,
[418] [419] [420] [421] [422] [423] [424] [425]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29177--29177
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[426] [427] [428] [429]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 29460--29462
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[430] [431]
Underfull \hbox (badness 7558) in paragraph at lines 29676--29680
[]\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 29686--29688
[]\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
[432]
Underfull \hbox (badness 5417) in paragraph at lines 29691--29694
[][][]\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 29695--29697
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[433] [434] [435] [436] [437] [438]
Underfull \hbox (badness 10000) in paragraph at lines 30105--30109
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[451] [452] [453]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[454]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31206--31206
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[455]
Underfull \hbox (badness 1158) in paragraph at lines 31310--31315
[]\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
[456]
Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 31337--31343
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[457]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 31413--31418
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[458]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31495--31495
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[459] [460] [461]
Underfull \hbox (badness 2809) in paragraph at lines 31759--31765
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 31766--31769
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473]
Underfull \hbox (badness 1735) in paragraph at lines 32578--32584
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[474]
Underfull \hbox (badness 4303) in paragraph at lines 32594--32597
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[475] [476] [477] [478] [479]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 32915--32915
 []         \T1/pcr/m/n/10 method = c("shell", "quick", "radix"), index.return 
= FALSE)[] 
[480] [481] [482]
Underfull \hbox (badness 2512) in paragraph at lines 33187--33189
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[483] [484] [485] [486]
Underfull \vbox (badness 10000) has occurred while \output is active [487]
[488]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33581--33581
 []\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)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33596--33596
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[489] [490] [491] [492] [493] [494]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34031--34031
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34032--34032
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[495] [496] [497]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 34238--34238
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[498]
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 34322--34332
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 34322--34332
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[499]
Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 1728) in paragraph at lines 34379--34386
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 34379--34386
\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 34379--34386
\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
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[504] [505] [506]
Underfull \hbox (badness 1163) in paragraph at lines 34851--34858
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 34851--34858
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[507] [508] [509] [510]
Underfull \hbox (badness 1142) in paragraph at lines 35123--35129
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 35138--35138
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[511] [512] [513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35384--35384
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[514]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35428--35428
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[515] [516] [517] [518] [519] [520] [521]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 35860--35860
 []\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 35863--35863
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[522]
Underfull \hbox (badness 10000) in paragraph at lines 35908--35911
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35955--35955
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[523] [524] [525] [526]
Underfull \hbox (badness 2762) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 36190--36199
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[527]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 36252--36252
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[528] [529]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36417--36417
 []\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. 
[530]
Underfull \hbox (badness 3219) in paragraph at lines 36500--36505
[]\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 36500--36505
\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
[531] [532]
Underfull \hbox (badness 2452) in paragraph at lines 36590--36593
\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 36590--36593
\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
[533] [534]
Underfull \hbox (badness 10000) in paragraph at lines 36777--36781
[]\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
[535]
Underfull \hbox (badness 1584) in paragraph at lines 36792--36795
[]\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
[536] [537] [538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36985--36985
 []\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 
[539] [540]
Underfull \hbox (badness 1082) in paragraph at lines 37120--37123
[]\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
[541] [542] [543]
Underfull \hbox (badness 1038) in paragraph at lines 37308--37311
[]\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
[544] [545] [546] [547] [548]
Underfull \hbox (badness 1515) in paragraph at lines 37647--37650
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[549] [550]
Underfull \hbox (badness 1924) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[551]
Underfull \hbox (badness 4096) in paragraph at lines 37869--37872
[]\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 ,
[552] [553] [554]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38103--38103
 []            \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 38105--38105
 []            \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),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 38107--38107
 []                 \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)))))[] 
[555]
Underfull \hbox (badness 10000) in paragraph at lines 38120--38122
[]\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
[556]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[557] [558]
Underfull \hbox (badness 1867) in paragraph at lines 38318--38322
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 38380--38384
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[559] [560] [561] [562] [563]
Underfull \hbox (badness 1371) in paragraph at lines 38726--38730
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val
id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z
one col-
Underfull \hbox (badness 1648) in paragraph at lines 38726--38730
\T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see []
[]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _
[564]
Underfull \hbox (badness 5637) in paragraph at lines 38799--38808
[]\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 Ol-son/IANA
Underfull \hbox (badness 1629) in paragraph at lines 38799--38808
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 38809--38816
[]\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 38809--38816
\T1/ptm/m/n/10 fault on OS X and Win-dows: rec-om-mended on So-laris), the data
base at
Underfull \hbox (badness 1303) in paragraph at lines 38809--38816
\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 '
[565]
Underfull \hbox (badness 10000) in paragraph at lines 38873--38875
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / www . twinsun .
[566] [567] [568]
Underfull \hbox (badness 10000) in paragraph at lines 39087--39089
[]\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
[569] [570]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 39209--39209
 []\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 39211--39211
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[571] [572] [573] [574] [575]
Underfull \hbox (badness 6542) in paragraph at lines 39547--39549
[]\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
[576] [577]
Underfull \hbox (badness 1708) in paragraph at lines 39706--39714
[]\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 39706--39714
\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 10000) in paragraph at lines 39715--39719
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 39715--39719
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 39715--39719
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 39729--39734
[][][]\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;
[578] [579]
Underfull \hbox (badness 3895) in paragraph at lines 39791--39803
[]\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 39791--39803
\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 ,
[580] [581]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[582] [583]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 40117--40117
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 1803) in paragraph at lines 40650--40653
[]\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 ),
Underfull \hbox (badness 2334) in paragraph at lines 40654--40661
[]\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
Underfull \hbox (badness 4726) in paragraph at lines 40680--40684
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 40680--40684
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[592] [593] [594]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[595] [596] [597] [598]
Underfull \hbox (badness 6220) in paragraph at lines 41143--41148
[]\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 41143--41148
\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,
Underfull \hbox (badness 1533) in paragraph at lines 41143--41148
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
Underfull \hbox (badness 6592) in paragraph at lines 41159--41164
[]\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
[599]
Underfull \hbox (badness 1603) in paragraph at lines 41178--41182
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[600]
Underfull \hbox (badness 10000) in paragraph at lines 41243--41246
[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
Underfull \hbox (badness 10000) in paragraph at lines 41243--41246
\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 2818) in paragraph at lines 41249--41253
[]\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
[601]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41282--41282
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[602] [603] [604] [605] [606]
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[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[607]
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[]\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
[608]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
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[]\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
[609]) (./compiler-pkg.tex [610]
Chapter 2.
[611] [612] [613]) (./datasets-pkg.tex [614]
Chapter 3.
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[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[615] [616] [617] [618] [619]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[620]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[621] [622] [623] [624] [625]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[626] [627]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[628] [629] [630] [631]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[632] [633] [634] [635] [636]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[637] [638]
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[]\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 ,
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\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
[639]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[640] [641]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[642]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[643] [644]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[645] [646] [647] [648]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[649] [650] [651] [652] [653] [654] [655] [656]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2674--2677
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[657]
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[658]
Underfull \vbox (badness 1789) has occurred while \output is active [659]
[660]
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[661] [662]
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[663]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[664] [665] [666] [667] [668] [669] [670]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3548--3548
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[671] [672]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[673]
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[674]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[675]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[676] [677] [678] [679] [680] [681] [682] [683] [684] [685]
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[687] [688]) (./grDevices-pkg.tex
Chapter 4.
[689] [690] [691] [692] [693] [694]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[695]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[696] [697] [698] [699] [700] [701] [702] [703] [704]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[705]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[706]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[707]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[708]
Underfull \hbox (badness 1173) in paragraph at lines 1268--1271
[]\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
[709] [710] [711]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[712]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[713] [714] [715]
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[]\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 1756--1761
\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
[716]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[717]
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[]\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-
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\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 ,
[718]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[719] [720]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[721] [722]
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\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
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\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
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\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
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\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
[723]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[724] [725] [726] [727] [728] [729]
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[730] [731] [732] [733] [734] [735]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[736] [737] [738] [739]
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 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[740]
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[]\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
[741]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[742] [743] [744] [745]
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[]\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 ,
[746] [747] [748] [749] [750]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[751] [752]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[753]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[754] [755]
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[756]
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[]\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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[757]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[758]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[759] [760]
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[]\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
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[][][]\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
[761] [762]
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\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 ,
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\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 ,
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\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 ),
[763]
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\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
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[]\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 /
[764] [765]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[766]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[767] [768]
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[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[769] [770] [771] [772] [773]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[774] [775] [776] [777] [778] [779]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\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
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\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[782]
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[]\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
[783]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[784] [785]
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\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 ,
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[]\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 /
[786] [787] [788]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
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[]\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
[789] [790] [791]) (./graphics-pkg.tex [792]
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[793] [794] [795] [796]
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[]\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-
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[]\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
[800] [801] [802]
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[]\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
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[][]\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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[803]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[804] [805]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[806] [807] [808] [809] [810] [811] [812]
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 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
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\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
[813]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[814]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
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 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
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 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[815] [816] [817] [818] [819]
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[][][]\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
[820]
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[821]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[822] [823]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[824] [825] [826] [827] [828]
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\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
[829] [830] [831] [832] [833]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
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[][][]\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
[838] [839] [840]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[841]
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[]\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
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[842] [843] [844]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[845]
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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[846] [847]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[848]
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 = c(0, 0.3))[] 
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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[850]
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[][][]\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
[851] [852]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[853] [854] [855]
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[]\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
[856] [857] [858] [859]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[860]
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\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
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[]\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
[861]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 
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=c(2,2,3,2))[] 
[862]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[863]
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\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 ,
[864] [865]
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[]\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.
[866]
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</builddir/build/BUILD/R-3.3.0/library/graphics/help/figures/mai.pdf, id=28625,
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[870]
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[]\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
[871]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[872]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[873]
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[874] [875] [876]
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 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[877]
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 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
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[]\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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[878] [879] [880] [881]
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 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[] 
[882] [883] [884]
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 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[885] [886] [887] [888] [889] [890]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[891] [892]
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[]\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
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[][] 
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[894]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[896]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[897]
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[]\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
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[901]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[902] [903] [904] [905] [906] [907]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[908]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[909] [910] [911] [912] [913]
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
[914]
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[915] [916]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[917] [918]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
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[]\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
[919] [920]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[921] [922]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[923] [924]
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 []     \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�...")[] 
[925]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\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
[926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [927]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[928] [929]
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 []\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)[] 
[930]) (./grid-pkg.tex
Chapter 6.
[931] [932] [933] [934] [935] [936]
Underfull \hbox (badness 10000) in paragraph at lines 383--389
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\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
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
Underfull \vbox (badness 10000) has occurred while \output is active [947]
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[]\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-
[948] [949] [950]
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[]\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
[951] [952] [953] [954] [955] [956] [957]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[958] [959] [960]
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[961]
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[]\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 ,
[962]
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[]\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-
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[]\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
[963] [964] [965]
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[]\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
[966] [967] [968]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
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[]\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-
[969] [970] [971]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[972] [973] [974] [975]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[976] [977] [978] [979] [980]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[981]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[982]
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[]\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
[983]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[984]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[985] [986] [987]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[988] [989] [990] [991] [992] [993] [994] [995] [996]
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[]\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-
[997] [998] [999]
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[]\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
[1000]
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[]\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-
[1001] [1002] [1003]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012]
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[]\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
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
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\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1024] [1025] [1026] [1027] [1028]
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[]\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
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[][][]\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 ,
[1029] [1030]
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[]\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
[1031] [1032] [1033] [1034]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1035]) (./methods-pkg.tex [1036]
Chapter 7.
[1037] [1038] [1039]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1040] [1041] [1042] [1043] [1044] [1045]
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[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1046] [1047]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
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\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058]
[1059] [1060]
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
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[]\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
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("removeClass.msg", defaul
t=TRUE))[] 
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1068] [1069] [1070]
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[]\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
[1071]
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[]\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
[1072]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1073] [1074]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1075]
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
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 []            \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T
RUE))[] 
[1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083]
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[]\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
[1084]
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[]\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
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[]
[1085]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1086]
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\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1087] [1088] [1089]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1090] [1091] [1092]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1093] [1094]
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1095]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1096] [1097] [1098] [1099] [1100] [1101]
Underfull \hbox (badness 10000) in paragraph at lines 4975--4984
[]\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
[1102] [1103] [1104]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
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 []\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 5211--5211
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
[1106]
Underfull \hbox (badness 1033) in paragraph at lines 5281--5288
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1107]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1108] [1109] [1110] [1111]
Underfull \hbox (badness 1087) in paragraph at lines 5649--5654
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5662--5666
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5662--5666
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1112] [1113]
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5753--5757
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1114] [1115]
Underfull \hbox (badness 10000) in paragraph at lines 5940--5956
[]\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
[1116] [1117] [1118]
Underfull \hbox (badness 1248) in paragraph at lines 6237--6241
[]\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 6237--6241
\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
[1119] [1120]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
Underfull \hbox (badness 1072) in paragraph at lines 6469--6476
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1121] [1122] [1123]
Underfull \vbox (badness 10000) has occurred while \output is active [1124]
[1125]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6828 \aliasA{S4}{S3Part}{S4}
                               [1126] [1127] [1128]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7060--7060
 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7065--7065
 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
[1129]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7096 \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.7098 \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.7099 \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.7101 \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.7102 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7163--7167
[]\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
[1130]
Underfull \hbox (badness 6708) in paragraph at lines 7176--7188
[]\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 7176--7188
\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 7176--7188
\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 ,
[1131] [1132]
Underfull \hbox (badness 1694) in paragraph at lines 7336--7338
[]\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 7360--7363
[]\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
[1133] [1134] [1135] [1136] [1137] [1138]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7815--7815
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1139] [1140]
Underfull \hbox (badness 2277) in paragraph at lines 7950--7958
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing
[1141]
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[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
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[]\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
[1142] [1143] [1144] [1145] [1146]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8352--8352
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
Underfull \hbox (badness 1755) in paragraph at lines 8388--8391
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1147] [1148]
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 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1149] [1150] [1151] [1152] [1153]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8937--8937
 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
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 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1154]
[1155]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9048--9048
 []\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 9059--9059
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1156] [1157] [1158] [1159] [1160] [1161] [1162] [1163] [1164]
Underfull \hbox (badness 10000) in paragraph at lines 9757--9759
[]\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
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[]\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 9765--9769
\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
[1165] [1166] [1167] [1168]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\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
[1169]
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[]\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
[1170] [1171]
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[]\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
[1172]
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[]\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa
s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but
Underfull \hbox (badness 10000) in paragraph at lines 303--311
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1173] [1174]
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[]\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
[1175] [1176] [1177] [1178]
Underfull \hbox (badness 1917) in paragraph at lines 710--719
[]\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 710--719
\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
[1179] [1180]
Underfull \hbox (badness 10000) in paragraph at lines 847--850
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1181] [1182] [1183]
Underfull \hbox (badness 5388) in paragraph at lines 1036--1041
[]\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
[1184]
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[]\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
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 []\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)[] 
[1185] [1186]
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 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1254--1257
[]\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
[1187]
Underfull \hbox (badness 3375) in paragraph at lines 1300--1302
[]\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
[1188] [1189]) (./splines-pkg.tex [1190]
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
[1191] [1192] [1193] [1194] [1195] [1196] [1197]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1198] [1199] [1200] [1201]
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 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1202] [1203] [1204]) (./stats-pkg.tex
Chapter 10.
[1205]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1206] [1207] [1208] [1209] [1210]
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1211] [1212] [1213] [1214] [1215] [1216]
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[]\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
[1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225]
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[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1226]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1506--1510
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
Underfull \hbox (badness 10000) in paragraph at lines 2079--2084
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
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\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
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\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1236]
Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1237] [1238] [1239] [1240]
Underfull \hbox (badness 1221) in paragraph at lines 2431--2436
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2431--2436
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1241]
Underfull \hbox (badness 3965) in paragraph at lines 2508--2510
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1242] [1243]
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 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1244] [1245] [1246] [1247]
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 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1248] [1249] [1250]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3076--3078
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1251]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3123--3123
 []\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 3124--3124
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1252] [1253] [1254] [1255] [1256]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3502--3502
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1257] [1258] [1259] [1260]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3772--3772
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1261] [1262] [1263] [1264] [1265]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4057--4057
 []\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 4058--4058
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1266] [1267] [1268] [1269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4293--4293
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1270] [1271]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4461--4461
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1272] [1273]
Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
[1274] [1275] [1276] [1277] [1278]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4913--4913
 []\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 4915--4915
 []\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))[] 
[1279]
Underfull \hbox (badness 7397) in paragraph at lines 5002--5006
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5002--5006
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1280] [1281]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5136--5136
 []\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 5154--5154
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1282]
Underfull \hbox (badness 2680) in paragraph at lines 5181--5183
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5186--5188
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1283] [1284] [1285]
Underfull \hbox (badness 1436) in paragraph at lines 5364--5369
[]\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 5364--5369
\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 5364--5369
\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 ,
[1286] [1287]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5550--5550
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1288]
Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1289] [1290]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5716--5716
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1291] [1292] [1293]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5901--5901
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1294] [1295] [1296]
Underfull \hbox (badness 10000) in paragraph at lines 6064--6069
[]\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
[1297] [1298] [1299]
Underfull \hbox (badness 5954) in paragraph at lines 6260--6262
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1300]
Underfull \hbox (badness 2503) in paragraph at lines 6342--6345
[]\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 6346--6348
[]\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 6349--6354
\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 6384--6387
[][][]\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
[1301]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6419--6419
 []\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 6434--6434
 []\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):[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6449--6449
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1303] [1304] [1305]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6690--6690
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1306] [1307] [1308] [1309] [1310] [1311]
Underfull \hbox (badness 10000) in paragraph at lines 7062--7066
\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
[1312]
Underfull \hbox (badness 6493) in paragraph at lines 7159--7162
[]\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
[1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320]
Underfull \hbox (badness 10000) in paragraph at lines 7706--7711
[]\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 , ...,
[1321] [1322]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7844--7846
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1323] [1324] [1325]
Underfull \hbox (badness 1210) in paragraph at lines 8061--8063
[]\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
[1326] [1327] [1328] [1329] [1330] [1331] [1332]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8505--8505
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8527--8527
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8530--8530
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1333] [1334]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8668--8668
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1335]
Underfull \hbox (badness 1859) in paragraph at lines 8707--8712
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1336] [1337] [1338] [1339] [1340]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9060--9060
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1341] [1342]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1343] [1344] [1345] [1346] [1347] [1348] [1349]
Underfull \hbox (badness 2443) in paragraph at lines 9680--9686
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1350] [1351] [1352]
Underfull \hbox (badness 3758) in paragraph at lines 9894--9897
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1353] [1354] [1355] [1356]
Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1357]
Underfull \hbox (badness 4132) in paragraph at lines 10194--10198
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1358]
Underfull \hbox (badness 10000) in paragraph at lines 10297--10300
[]\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
[1359] [1360] [1361]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1362]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1363]
Underfull \hbox (badness 10000) in paragraph at lines 10620--10626
[][][]\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,
Underfull \hbox (badness 1418) in paragraph at lines 10658--10663
\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 (=
[1364] [1365]
Underfull \hbox (badness 2635) in paragraph at lines 10791--10794
\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
[1366] [1367] [1368]
Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 10993--11002
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 10993--11002
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11075--11075
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1370]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11108--11108
 []            \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 11121--11125
[]\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
[1371] [1372] [1373]
Underfull \hbox (badness 7379) in paragraph at lines 11300--11303
[]\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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1374] [1375]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11439--11439
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1376]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11506--11506
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11518--11518
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1377]
Underfull \hbox (badness 1062) in paragraph at lines 11566--11571
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1378] [1379]
Underfull \hbox (badness 3623) in paragraph at lines 11711--11713
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1380]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11799--11799
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1381] [1382]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11892--11892
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1383]
Underfull \hbox (badness 10000) in paragraph at lines 11940--11943
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1384] [1385] [1386]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\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
[1387]
Underfull \hbox (badness 2753) in paragraph at lines 12232--12234
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1388] [1389]
Underfull \hbox (badness 1292) in paragraph at lines 12357--12361
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1390] [1391]
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\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 12476--12480
\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
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Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1402] [1403] [1404]
Underfull \hbox (badness 10000) in paragraph at lines 13365--13369
[]\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
 ,
[1405] [1406] [1407]
Underfull \hbox (badness 6995) in paragraph at lines 13550--13552
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1408] [1409]
Underfull \hbox (badness 1163) in paragraph at lines 13698--13706
\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 ,
[1410] [1411]
Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1412] [1413]
Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 13956--13960
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1414]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14004--14004
 []\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 14005--14005
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1415]
Underfull \hbox (badness 10000) in paragraph at lines 14060--14063
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14060--14063
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1416] [1417] [1418] [1419]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14346--14346
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
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 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1420]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14397--14399
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14440--14440
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1421] [1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 2726) in paragraph at lines 14843--14846
[]\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 ,
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15555--15555
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1439] [1440]
Underfull \hbox (badness 1648) in paragraph at lines 15746--15748
[]\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,
[1441]
Underfull \hbox (badness 2591) in paragraph at lines 15760--15769
\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 15760--15769
\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
[1442]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15824--15824
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16377--16377
 []\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[] 
[1451] [1452] [1453]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16605--16605
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1454] [1455] [1456] [1457] [1458] [1459] [1460]
Underfull \hbox (badness 2772) in paragraph at lines 17038--17041
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
Underfull \hbox (badness 10000) in paragraph at lines 17038--17041
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1461] [1462]
Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1463]
Underfull \vbox (badness 10000) has occurred while \output is active [1464]
Underfull \vbox (badness 10000) has occurred while \output is active [1465]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17330--17330
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1466]
Underfull \hbox (badness 10000) in paragraph at lines 17410--17414
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1467]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17490--17490
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17537--17537
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17584--17584
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476]
Underfull \hbox (badness 1248) in paragraph at lines 18074--18077
[]\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 1127) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1477]
Underfull \hbox (badness 1478) in paragraph at lines 18095--18099
\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
Underfull \hbox (badness 2042) in paragraph at lines 18148--18150
[]\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
[1478] [1479]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18244--18244
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1480]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18286--18286
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18319--18319
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1481]
Underfull \hbox (badness 2564) in paragraph at lines 18357--18368
[]\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 18357--18368
\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
[1482]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18420--18420
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1483] [1484] [1485]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18635--18635
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1486]
Underfull \hbox (badness 1337) in paragraph at lines 18711--18714
[]\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
[1487] [1488] [1489] [1490] [1491]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19027--19027
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1492] [1493]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19115--19115
 []       \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 (6.78088pt too wide) in paragraph at lines 19118--19118
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1494] [1495] [1496] [1497] [1498]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19434--19434
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 4779) in paragraph at lines 19441--19443
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1499]
Underfull \hbox (badness 1107) in paragraph at lines 19502--19504
[]\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
[1500]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19557--19557
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19564--19564
 []\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)[] 
[1501]
Underfull \hbox (badness 10000) in paragraph at lines 19614--19617
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 19614--19617
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1502]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19658--19658
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1503] [1504]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19780--19780
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1505]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19886--19886
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1506]
Underfull \hbox (badness 10000) in paragraph at lines 19941--19943
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1507]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19978--19978
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
[1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518]
[1519] [1520]
Underfull \hbox (badness 6859) in paragraph at lines 20852--20859
[][][]\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 20863--20869
[]\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 ,
[1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]
[1532] [1533] [1534] [1535] [1536] [1537]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21875--21875
 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1538] [1539] [1540] [1541] [1542]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
[1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552]
Underfull \hbox (badness 1028) in paragraph at lines 22881--22884
[]\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
[1553] [1554]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22991--22994
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1555] [1556] [1557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23202--23202
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1558] [1559] [1560]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23422--23422
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1561] [1562]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\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
[1563]
Underfull \hbox (badness 2134) in paragraph at lines 23619--23623
[][][]\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 23632--23632
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1564] [1565] [1566] [1567] [1568] [1569] [1570]
Underfull \hbox (badness 2591) in paragraph at lines 24089--24095
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1571] [1572] [1573]
Underfull \hbox (badness 1867) in paragraph at lines 24286--24288
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1574]
Underfull \hbox (badness 10000) in paragraph at lines 24299--24301
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24333--24333
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1575] [1576] [1577]
Underfull \hbox (badness 2495) in paragraph at lines 24523--24532
[]\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 .
[1578]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24605--24605
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 24612--24614
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1579]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24699--24699
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1580]
Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
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\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1581] [1582]
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 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1583] [1584] [1585]
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 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1586]
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 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1587] [1588] [1589] [1590] [1591] [1592]
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 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1593] [1594]
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
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[]\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
[1596]
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[]\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
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[][][]\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
[1597]
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[]\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
[1598]
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[]\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
[1599]
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 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
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 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1600] [1601]
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 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
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 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1602]
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[]\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
[1603]
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[]\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
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[]\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
[1604]
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[]\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
[1605]
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
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[]\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
[1606]
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 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
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 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1607] [1608] [1609] [1610] [1611] [1612] [1613]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1614] [1615] [1616] [1617] [1618] [1619] [1620]
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[]\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
[1621] [1622] [1623]
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[]\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
[1624] [1625]
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[]\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
[1626]
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[]\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
[1627] [1628] [1629]
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[]\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)
[1630] [1631]
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[]\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
[1632] [1633]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1634] [1635]
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 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1636]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1637]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1638]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1639]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1640]
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[]\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
[1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648]
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1649]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1650] [1651] [1652] [1653]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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 []        \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 29495--29495
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1654] [1655]
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 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
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 []\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:[] 
[1656] [1657] [1658] [1659]
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[]\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
[1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667]
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[]\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
[1668]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1669] [1670] [1671] [1672] [1673]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
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 []      \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[] 
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[]\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
[1674] [1675]
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1676]) (./stats4-pkg.tex
Chapter 11.
[1677] [1678] [1679]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1680] [1681] [1682]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}
                                                   [1683]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1684] [1685]) (./tcltk-pkg.tex [1686]
Chapter 12.
[1687] [1688] [1689] [1690]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1691] [1692] [1693]
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[]\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
[1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1706]) (./tools-pkg.tex
Chapter 13.
[1707]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1708]
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[]\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
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[]\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
[1709]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1710]
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[]\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
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\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-
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\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 ,
[1711]
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 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
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[]\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
[1712] [1713] [1714]
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[][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer /
 en / opentype /
[1715] [1716] [1717] [1718] [1719] [1720]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
[1721]
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1722]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1723] [1724]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\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-
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[]\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
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1725]
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
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[]\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
[1726]
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[]\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
[1727]
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1728] [1729]
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 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
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 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
[1730]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1731] [1732] [1733]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.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1734]
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[]\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
[1735]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1736] [1737] [1738] [1739]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs
t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age
[1740]
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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
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[]\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-
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\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-
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\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
[1741]
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\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
[1742] [1743]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
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 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
[1744] [1745]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2519--2519
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
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[]\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
[1746] [1747] [1748] [1749] [1750] [1751]
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[]\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
[1752] [1753] [1754] [1755] [1756]
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 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1757] [1758] [1759]
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[]\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
[1760] [1761]
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 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
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 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1762] [1763]
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[]\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
[1764] [1765] [1766] [1767]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\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
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[]\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
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\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
[1768]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1769] [1770] [1771]
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 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
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\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 ,
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[]\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
[1772]
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[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1773] [1774]) (./utils-pkg.tex
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 ',
[1775] [1776] [1777]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1778]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1779] [1780] [1781]
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[]\T1/ptm/m/n/10 Kurt Hornik and Dun-can Mur-doch (2011), Watch your spelling! 
\T1/ptm/m/it/10 The R Jour-nal \T1/ptm/b/n/10 3\T1/ptm/m/n/10 (2),
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 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1782]
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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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[]\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 ,
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\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-
[1783] [1784]
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\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
[1785]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1786]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1787] [1788]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1789]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1790] [1791] [1792] [1793] [1794] [1795]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1796]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1797]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1798] [1799]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1800]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1801] [1802]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1803]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1804]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1805]
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[][][]\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;
[1806]
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[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2209--2216
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1807]
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[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1808] [1809] [1810]
Underfull \hbox (badness 10000) in paragraph at lines 2399--2401
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1811] [1812] [1813]
Underfull \hbox (badness 10000) in paragraph at lines 2635--2639
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1814]
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[]\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
[1815]
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 []\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 '[] 
[1816]
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[]\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
[1817] [1818] [1819] [1820] [1821] [1822]
Underfull \hbox (badness 1072) in paragraph at lines 3246--3254
[]\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
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[]\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 3296--3301
\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
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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1823] [1824]
Underfull \hbox (badness 4660) in paragraph at lines 3401--3404
\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
[1825] [1826] [1827]
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[]\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
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1828]
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 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1829] [1830] [1831] [1832] [1833]
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 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1834]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4109 ...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.4109 ...mat Unordered and Ordered Lists}{format}
                                                   [1835] [1836] [1837]
[1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848]
[1849]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5018--5018
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1850]
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[]\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
[1851]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1852] [1853]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\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
[1854]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
[1855] [1856]
Underfull \hbox (badness 3118) in paragraph at lines 5524--5526
[]\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
[1857]
Underfull \hbox (badness 2409) in paragraph at lines 5557--5561
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1858]
Underfull \hbox (badness 5091) in paragraph at lines 5661--5663
[]\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
Overfull \hbox (44.55087pt too wide) in paragraph at lines 5677--5682
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 
[1859]
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5690--5697
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1860]
Underfull \hbox (badness 10000) in paragraph at lines 5807--5811
[]\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 1708) in paragraph at lines 5807--5811
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the ap-pro-pri-ate bi-nary type where
Underfull \hbox (badness 2376) in paragraph at lines 5821--5828
[]\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 5821--5828
\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 5821--5828
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1861]
Underfull \hbox (badness 1314) in paragraph at lines 5880--5887
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 5901--5906
[][][]\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 ,
[1862]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5922--5922
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
Underfull \hbox (badness 5133) in paragraph at lines 5958--5962
[]\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 5970--5973
[]\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
[1863]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6017--6017
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1864]
Underfull \hbox (badness 4132) in paragraph at lines 6098--6100
[]\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
[1865] [1866] [1867]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6256--6256
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1868] [1869]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6399--6399
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1870]
Underfull \hbox (badness 10000) in paragraph at lines 6439--6441
[]\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
[1871] [1872]
Underfull \hbox (badness 10000) in paragraph at lines 6580--6582
[]\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 6585--6587
[]\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
[1873] [1874] [1875]
Underfull \hbox (badness 1859) in paragraph at lines 6808--6811
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1876]
Underfull \hbox (badness 1655) in paragraph at lines 6890--6893
[]\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 6901--6901
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
[1877]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6905--6905
 []\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 6913--6913
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1878] [1879] [1880] [1881]
Underfull \hbox (badness 10000) in paragraph at lines 7203--7205
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7208--7213
[]\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,
[1882] [1883]
Underfull \hbox (badness 10000) in paragraph at lines 7359--7364
[]\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 7359--7364
[][]\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
[1884]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7369
[]\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 7366--7369
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1885]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7482--7482
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7483--7483
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1886] [1887] [1888] [1889]
Underfull \hbox (badness 1789) in paragraph at lines 7758--7760
[]\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
[1890]
Underfull \hbox (badness 10000) in paragraph at lines 7816--7820
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7816--7820
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1891] [1892]
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7929--7933
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1893]
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7992--7996
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1894] [1895] [1896] [1897]
Underfull \hbox (badness 5203) in paragraph at lines 8319--8322
[]\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
[1898]
Underfull \vbox (badness 4647) has occurred while \output is active [1899]
[1900]
Underfull \hbox (badness 1776) in paragraph at lines 8545--8552
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1901]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8569--8569
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1902] [1903]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8730--8730
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1904] [1905]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8911--8911
 []\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[] 
[1906] [1907]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8997--8997
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9000--9000
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9005--9005
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1908]
Underfull \hbox (badness 1077) in paragraph at lines 9077--9080
[]\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
[1909] [1910] [1911] [1912] [1913] [1914]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9517--9517
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1915]
Underfull \hbox (badness 10000) in paragraph at lines 9604--9606
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1916] [1917]
Underfull \hbox (badness 2181) in paragraph at lines 9727--9731
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 9727--9731
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 9739--9743
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1918]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9757--9757
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9761--9761
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1919] [1920]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9893--9893
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1921] [1922] [1923]
Underfull \hbox (badness 8075) in paragraph at lines 10093--10095
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
Underfull \hbox (badness 6725) in paragraph at lines 10143--10152
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 10143--10152
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 10143--10152
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1924] [1925]
Underfull \hbox (badness 3646) in paragraph at lines 10269--10271
[][][]$\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 /
[1926] [1927] [1928]
Underfull \hbox (badness 10000) in paragraph at lines 10447--10451
[]\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 10478--10484
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1929]
Underfull \hbox (badness 2012) in paragraph at lines 10573--10579
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1930]
Underfull \hbox (badness 2096) in paragraph at lines 10586--10588
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 10589--10591
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 10596--10599
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 10600--10603
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10654--10654
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
Underfull \hbox (badness 10000) in paragraph at lines 10661--10663
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
[1931]
Underfull \hbox (badness 1009) in paragraph at lines 10666--10677
[]\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
[1932]
Underfull \hbox (badness 2846) in paragraph at lines 10753--10763
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1933] [1934]
Underfull \hbox (badness 10000) in paragraph at lines 10902--10905
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1935]
Underfull \hbox (badness 2158) in paragraph at lines 10981--10984
[]\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
[1936] [1937] [1938]
Underfull \hbox (badness 3333) in paragraph at lines 11161--11163
[]\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-
[1939] [1940]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11322--11322
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1941]
Underfull \hbox (badness 5970) in paragraph at lines 11350--11353
[]\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 11350--11353
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11361--11370
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1942]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 11405--11405
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1943] [1944]
Underfull \hbox (badness 10000) in paragraph at lines 11529--11531
[]\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
[1945] [1946]
Underfull \hbox (badness 4492) in paragraph at lines 11683--11690
[]\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 11683--11690
\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 2452) in paragraph at lines 11683--11690
\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$"\T1/ptm/m/n/10 ) and
[1947] [1948]
Underfull \hbox (badness 2020) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11843--11859
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1949]
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[][][]$\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 .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957]
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[]\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
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\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 12454--12458
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
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[]\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 passed to
Underfull \hbox (badness 1052) in paragraph at lines 12463--12465
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1958]
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[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
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[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
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\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
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[]\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
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[][][]\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 ,
[1959] [1960] [1961] [1962]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12780--12780
 []\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:[]
 
[1963]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
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[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1964]
Underfull \hbox (badness 1715) in paragraph at lines 12866--12869
[]\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
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12923--12927
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1965] [1966] [1967]) [1968] [1969] [1970] (./KernSmooth-pkg.tex
Chapter 15.
[1971]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[1972] [1973] [1974] [1975] [1976]
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, 
[1977] [1978] [1979] [1980]) (./MASS-pkg.tex
Chapter 16.
[1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991]
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))[] 
[1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002]
[2003]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2015] [2016] [2017] [2018]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2019] [2020] [2021]
Underfull \hbox (badness 7362) in paragraph at lines 2863--2868
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/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/ptm/m/n/10 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2022] [2023]
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[]\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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2024] [2025] [2026]
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
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[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2027]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038]
[2039]
Underfull \hbox (badness 1845) in paragraph at lines 4162--4164
[]\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
[2040] [2041] [2042] [2043] [2044] [2045] [2046]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2047] [2048]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2049]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2050] [2051] [2052] [2053] [2054]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
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[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2055]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2064]
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 []\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") 
[2065] [2066]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...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.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2067]
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[]\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
[2068] [2069] [2070] [2071]
Underfull \vbox (badness 10000) has occurred while \output is active [2072]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2073]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2074] [2075] [2076] [2077] [2078] [2079]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2080]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\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 ) =
[2081]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2082] [2083]
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\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
[2084] [2085]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2086]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2087] [2088] [2089] [2090] [2091] [2092]
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[]\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
Underfull \hbox (badness 1515) in paragraph at lines 7996--8000
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2093] [2094]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8123--8127
[]\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
[2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105]
[2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2115]
Underfull \hbox (badness 1158) in paragraph at lines 9629--9632
[]\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),
[2116]
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 []\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 9713--9713
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9716--9716
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127]
[2128] [2129]) (./Matrix-pkg.tex [2130]
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
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2131]
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[]\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
[2132]
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[]\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
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\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
[2133]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\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
[2134] [2135]
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--497
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2136]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\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
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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2137] [2138]
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[]\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 .
[2139] [2140] [2141]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2142]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
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\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
[2143]
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2144]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1094 ...- '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.1094 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2145pdfTeX 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.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:pdfTeX warning (ext4): des
tination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has b
een already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:pdfTeX warning (ext4): des
tination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has b
een already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1176 \item[chol]
                   \code{signature(x = "dppMatrix")}:]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2146]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2147]
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[]\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
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[]\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
[2148]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
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 []\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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2149]
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[]\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 3861) in paragraph at lines 1491--1498
\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 1526--1530
[]\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
[2150]
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\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
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1583 ... 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.1583 ... 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.1584 \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.1605 \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.1616 \aliasA{rowSums}{colSums}{rowSums}
                                          [2151]
Underfull \hbox (badness 2922) in paragraph at lines 1670--1674
[]\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
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\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 1681--1684
[][][]\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
[2152]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2153]
Underfull \hbox (badness 3547) in paragraph at lines 1835--1838
[]\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
[2154] [2155] [2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 2072--2074
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 2194--2196
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2255--2259
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2159]
Underfull \hbox (badness 4713) in paragraph at lines 2290--2292
[]\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
[2160]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2161] [2162]
Underfull \hbox (badness 10000) in paragraph at lines 2507--2511
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2507--2511
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
Underfull \hbox (badness 2707) in paragraph at lines 2563--2567
[]\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 2568--2572
[]\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
[2163]
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[]\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 ;
Underfull \hbox (badness 2689) in paragraph at lines 2628--2630
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2164]
Underfull \hbox (badness 1097) in paragraph at lines 2654--2657
[]\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''
[2165]
Underfull \hbox (badness 3646) in paragraph at lines 2902--2905
[]\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 2924--2925
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2934--2936
[]\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 3803) in paragraph at lines 2937--2941
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2166]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 2953--2957
[]\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 2963--2967
[][][]\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
[2167] [2168]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2169] [2170]
Underfull \hbox (badness 1168) in paragraph at lines 3306--3309
[]\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
[2171]
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[]\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
[2172]
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3476--3478
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2173] [2174]
Underfull \hbox (badness 10000) in paragraph at lines 3668--3673
[]\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 3668--3673
\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
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2175]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2176]
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[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2177]
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[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2178]
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 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
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[]\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
[2179]
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[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
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[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2180] [2181] [2182] [2183]
Underfull \hbox (badness 10000) in paragraph at lines 4325--4330
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2184] [2185]
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 [] \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 4462--4462
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4476--4476
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2186] [2187]
Underfull \hbox (badness 10000) in paragraph at lines 4631--4633
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2188] [2189]
Underfull \hbox (badness 10000) in paragraph at lines 4778--4783
[]\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 ,
[2190]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4859--4859
 []\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 4861--4861
 []  \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 4865--4865
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4872--4872
 []  \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 '[] 
[2191] [2192]
Underfull \hbox (badness 4120) in paragraph at lines 5011--5014
[]\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
[2193]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5048--5048
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5053--5053
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5060--5060
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
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 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2194]
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[]\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
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2195]
Underfull \hbox (badness 3138) in paragraph at lines 5220--5222
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2196]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5284--5284
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5305--5307
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5313--5318
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2197] [2198] [2199]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5542--5542
 []\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[] 
[2200]
Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[][][]\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 5634--5634
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2201]
Underfull \hbox (badness 1622) in paragraph at lines 5671--5676
[]\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 5671--5676
\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
[2202] [2203]
Underfull \hbox (badness 1062) in paragraph at lines 5857--5860
[]\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
[2204]
Underfull \hbox (badness 2809) in paragraph at lines 5886--5889
[]\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
[2205]
Underfull \hbox (badness 2635) in paragraph at lines 5998--6003
[]\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 5998--6003
\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 6006--6009
[]\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.,
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6127
\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 6117--6127
[][]\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
[2207]
Underfull \hbox (badness 1184) in paragraph at lines 6199--6202
[]\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
[2208]
Underfull \hbox (badness 10000) in paragraph at lines 6297--6300
[]\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.,
[2209]
Underfull \hbox (badness 10000) in paragraph at lines 6372--6375
[]\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 6388--6388
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2210]
Underfull \hbox (badness 2443) in paragraph at lines 6427--6433
[]\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 6427--6433
[][]\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 6448--6451
[]\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
[2211]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6518--6518
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2212] [2213]
Underfull \hbox (badness 6268) in paragraph at lines 6654--6657
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2214]
Underfull \hbox (badness 5036) in paragraph at lines 6678--6682
[]\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 6678--6682
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2215]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6771 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6847--6850
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6852--6855
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 6852--6855
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
Underfull \hbox (badness 10000) in paragraph at lines 6870--6873
Underfull \hbox (badness 7326) in paragraph at lines 6880--6882
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2216]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.6942 ...*\%}{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.7050 ...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.7150 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2217]
Underfull \hbox (badness 1881) in paragraph at lines 7248--7254
\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
[2218pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7310 \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.7310 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7320--7323
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7320--7323
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7323--7328
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7332--7334
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7334--7336
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7338--7339
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2219] [2220]
Underfull \hbox (badness 1062) in paragraph at lines 7519--7522
[]\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
[2221]
Underfull \hbox (badness 2809) in paragraph at lines 7553--7556
[]\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
[2222]
Underfull \hbox (badness 10000) in paragraph at lines 7605--7607
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2223]
Underfull \hbox (badness 1406) in paragraph at lines 7645--7649
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7645--7649
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2224]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7743--7743
 []\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 [2225]
Underfull \hbox (badness 2635) in paragraph at lines 7808--7813
[]\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 7808--7813
\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 7816--7819
[]\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.,
[2226] [2227]
Underfull \hbox (badness 10000) in paragraph at lines 8010--8012
[]\T1/ptm/m/n/10 fast
[2228]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8050 \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.8050 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2229]
Underfull \hbox (badness 2401) in paragraph at lines 8231--8241
[]\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 ,
[2230]
Underfull \hbox (badness 1184) in paragraph at lines 8302--8305
[]\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
[2231]
Underfull \hbox (badness 10000) in paragraph at lines 8392--8395
[]\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.,
[2232]
Underfull \hbox (badness 10000) in paragraph at lines 8468--8471
[]\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 8484--8484
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2233] [2234]
Underfull \hbox (badness 10000) in paragraph at lines 8594--8596
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
Underfull \hbox (badness 1596) in paragraph at lines 8610--8612
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
Underfull \hbox (badness 1721) in paragraph at lines 8616--8620
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2235]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8695--8695
 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8700--8700
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8705--8705
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2236]
Underfull \hbox (badness 3989) in paragraph at lines 8728--8738
[]\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 8728--8738
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2237]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8829 \aliasA{qr}{qr-methods}{qr}
                                   [2238]
Underfull \hbox (badness 5119) in paragraph at lines 8873--8876
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
Overfull \hbox (36.7804pt too wide) in paragraph at lines 8894--8894
 []                  \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)),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 8911--8911
 []          \T1/pcr/m/n/9 all.equal(qr.coef(qxr, y), cf <- c(int=6, b1=-3, c1=
-2, c2=-1), tol=1e-15)[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 8915--8915
 []          \T1/pcr/m/n/9 all.equal(unname(qcfXy), unname(cf), tol=1e-15) || #
 FAIL names: ## FIXME_______[] 
[2239]
Overfull \hbox (139.38028pt too wide) in paragraph at lines 8918--8918
 []          \T1/pcr/m/n/9 all.equal(unname(m(qcfXY)), unname(m(cf)), tol=1e-15
) || # FAIL dimnames: ## FIXME_______[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8936--8936
 []\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 (15.18042pt too wide) in paragraph at lines 8941--8941
 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co
rrect colnames[] 
[2240]
Underfull \hbox (badness 10000) in paragraph at lines 8991--8997
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
Underfull \hbox (badness 10000) in paragraph at lines 9008--9011
[]\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
[2241]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9079--9079
 []\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"[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9100--9100
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9101--9101
 []\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.9116 ... the Reciprocal Condition Number}{rcond}
                                                   [2242] [2243]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2244] [2245] [2246]
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[]\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
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\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2247] [2248]
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[]\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
[2249]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9691 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2251]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2252]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9960--9960
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2253]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\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,
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[]\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)
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\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
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\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
[2254]
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[]\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
[2255]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2256] [2257]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2258]
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[]\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
[2259]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2260]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\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)[] 
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 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
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 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
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 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2261]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
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[][][]\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
[2262]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10685 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2263]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2264]
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 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2265]
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[]\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-
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\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 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2266]
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[]\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
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[]\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
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2267] [2268]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
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[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2269]
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[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
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[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
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[]\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 1259) in paragraph at lines 11291--11296
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11299--11304
\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
[2270]
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[]\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.,
[2271]
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[]\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
[2272]
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[]\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
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\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
[2273]
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[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2274] [2275] [2276]
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[]\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
[2277]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\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)[] 
[2278] [2279]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2280] [2281] [2282]) (./boot-pkg.tex
Chapter 18.
[2283] [2284] [2285] [2286] [2287] [2288] [2289]
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 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2290]
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[]\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
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[]\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-
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\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2291]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2292]
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\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2293]
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[]\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.
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[][][]\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 ,
[2294]
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 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
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[2296]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2297]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\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
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\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
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2298] [2299] [2300] [2301] [2302]
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[]\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-
[2303] [2304] [2305] [2306]
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 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2307] [2308] [2309] [2310]
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 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2312] [2313] [2314] [2315]
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
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.
[2316]
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 ,
[2317]
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
[2318] [2319] [2320] [2321] [2322]
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,[] 
[2323] [2324] [2325]
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 ,
[2326]
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)) 
[2327] [2328] [2329]
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 
[2330] [2331] [2332] [2333] [2334] [2335] [2336]
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)[] 
[2337] [2338]
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])[] 
[2339] [2340] [2341]
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
[2342]
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 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2343] [2344]
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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2345] [2346] [2347] [2348] [2349] [2350] [2351] [2352] [2353]
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
[2354] [2355] [2356] [2357]
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
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\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2358]
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])[] 
[2359] [2360] [2361] [2362] [2363] [2364] [2365] [2366]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2367]
Underfull \hbox (badness 1127) in paragraph at lines 5984--6002
\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
[2368]
Underfull \hbox (badness 2837) in paragraph at lines 6017--6020
[]\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
[2369] [2370] [2371] [2372]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6302--6302
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2373] [2374]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6491--6491
 []\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 6493--6493
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2375] [2376] [2377]
Underfull \hbox (badness 1596) in paragraph at lines 6738--6742
[]\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
[2378] [2379]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6898--6898
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2380] [2381] [2382] [2383] [2384] [2385] [2386] [2387]) (./class-pkg.tex
[2388]
Chapter 19.
[2389] [2390] [2391] [2392] [2393] [2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404]) (./cluster-pkg.tex
Chapter 20.
[2405]
Underfull \hbox (badness 3098) 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-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2406]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2407]
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]))[] 
[2408] [2409]
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[2411]
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,
 ...)[] 
[2412]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2413]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 636--636
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2414]
Underfull \hbox (badness 3078) in paragraph at lines 682--685
[]\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
[2415]
Underfull \hbox (badness 2941) in paragraph at lines 771--774
[][][]\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 
,
[2416]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 809--809
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2417]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
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 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, d.power = 1, verbose =
 interactive(), ...) 
[2418]
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[]\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 966--970
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2419] [2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1060--1060
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2421]
Underfull \hbox (badness 4144) in paragraph at lines 1136--1140
[]\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
[2422]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1212--1212
 []          \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 1218--1218
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2423] [2424]
Underfull \hbox (badness 10000) in paragraph at lines 1402--1405
[2425]
Underfull \hbox (badness 10000) in paragraph at lines 1419--1423
[][][]\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 1443--1443
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1452--1452
 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1460--1460
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2426]
Underfull \hbox (badness 5741) in paragraph at lines 1500--1503
[]\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
[2427] [2428]
Underfull \hbox (badness 5008) in paragraph at lines 1676--1684
\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
[2429]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1767--1767
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
[2430]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1786--1786
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2431] [2432] [2433] [2434]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
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Underfull \hbox (badness 3179) in paragraph at lines 2113--2119
[][][]\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.
[2435] [2436] [2437]
Underfull \hbox (badness 10000) in paragraph at lines 2271--2274
[][][]\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 ,
[2438]
Underfull \hbox (badness 1292) in paragraph at lines 2339--2342
[]\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 2348--2350
[]\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 2371--2374
[][][]\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 ,
[2439] [2440] [2441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2573--2573
 []\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 ):[] 
[2442] [2443] [2444]
Underfull \hbox (badness 1067) in paragraph at lines 2759--2764
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2814--2814
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2445] [2446]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2917--2917
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2447] [2448] [2449]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3113--3113
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3114--3114
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2450]
Underfull \hbox (badness 10000) in paragraph at lines 3181--3184
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2451]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3231--3231
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3232--3232
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2452] [2453] [2454]
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[]\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
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[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2455]
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[][][]\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 ,
[2456]
Underfull \hbox (badness 4621) in paragraph at lines 3542--3547
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3542--3547
\T1/ptm/m/n/10 which 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
Underfull \hbox (badness 6268) in paragraph at lines 3554--3557
[][][]\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 ,
[2457] [2458] [2459]
Underfull \hbox (badness 10000) in paragraph at lines 3739--3742
[][][]\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 3770--3773
[][][]\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 ,
[2460]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3823--3823
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
[2461]
Underfull \hbox (badness 2035) in paragraph at lines 3834--3836
[]\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
[2462] [2463] [2464]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4027--4027
 []     \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 4029--4029
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4058--4063
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 4125--4133
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2466]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4167--4167
 []\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 4176--4176
 []   \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 4178--4178
 []      \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 4181--4181
 []\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 4183--4183
 []   \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 4197--4197
 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474]) (./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,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2475]
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[]\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
[2476]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2477] [2478] [2479]) (./foreign-pkg.tex [2480]
Chapter 22.
[2481]
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
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2482] [2483]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2484]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2485] [2486] [2487]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 519--527
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2489]
Underfull \hbox (badness 7613) in paragraph at lines 537--543
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2490] [2491] [2492]
Underfull \hbox (badness 10000) in paragraph at lines 734--735
Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2493]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 820--820
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2494]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 884--884
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 910--913
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2495] [2496]
Underfull \hbox (badness 10000) in paragraph at lines 994--995
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1030--1030
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2497] [2498]
Underfull \hbox (badness 1286) in paragraph at lines 1115--1119
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2499]
Underfull \hbox (badness 10000) in paragraph at lines 1188--1194
[]\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 ,
[2500]) (./lattice-pkg.tex
Chapter 23.
[2501] [2502] [2503]
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 []       \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"),[] 
[2504]
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"),[] 
[2505]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
Underfull \hbox (badness 10000) in paragraph at lines 357--369
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2506]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2507] [2508]
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
[2509] [2510] [2511] [2512]
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.
[2513]
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
[2514] [2515]
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
[2516] [2517] [2518]
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 ,
[2519]
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 ,
[2520]
Underfull \vbox (badness 10000) has occurred while \output is active [2521]
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
[2522]
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
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[]\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
[2523]
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
[2524] [2525] [2526]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2527]
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[]\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
[2528] [2529] [2530]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2531] [2532] [2533]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2534] [2535]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2536]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2537]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\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 2793--2798
\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 2879--2883
[]\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 2879--2883
\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 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2538]
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[]\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 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
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\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 2961--2965
[]\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
[2539] [2540]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \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 3063--3063
 []      \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 3064--3064
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2541]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\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 3145--3152
\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
[2542] [2543] [2544] [2545]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2546]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2547] [2548] [2549] [2550] [2551]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2552]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2553] [2554]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\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
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[]\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 4107--4111
\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
[2555]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\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 4172--4176
\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
[2556] [2557]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\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 4286--4296
\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 4286--4296
\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 4286--4296
\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 4286--4296
\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 4311--4314
[]\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 4314--4316
[]\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
[2558] [2559] [2560] [2561] [2562] [2563]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2564] [2565]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\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 .
[2566] [2567]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\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
[2568] [2569] [2570] [2571] [2572] [2573]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\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 5399--5399
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2574]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\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 5488--5491
\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
Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2575]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\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
[2576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2577]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2578]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2579]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\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 5859--5866
[]\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 5859--5866
\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
[2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\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 ,
[2582] [2583]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2584] [2585]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\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 6275--6280
\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
[2586] [2587]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2588]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\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
[2589]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\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 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2590]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2591] [2592] [2593] [2594] [2595]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\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 6957--6964
\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
[2596]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2597]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\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 7057--7060
\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
[2598]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\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
[2599] [2600]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2601]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2602] [2603]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\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 7527--7530
[]\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
Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2604]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
 []       \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 7607--7607
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2605]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2606] [2607] [2608]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2609]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\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
Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2610] [2611] [2612] [2613] [2614] [2615] [2616] [2617]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\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 8467--8470
\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
[2618] [2619]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
 []\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 8643--8643
 []\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 8655--8655
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2620]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\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
[2621]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2622]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2623] [2624]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2625] [2626]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2627]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\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 (104.63074pt too wide) in paragraph at lines 9161--9165
\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
[2628] [2629] [2630] [2631] [2632] [2633] [2634]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\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 4518) in paragraph at lines 9619--9623
\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 ,
Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2635] [2636] [2637]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2638] [2639] [2640] [2641])
(./mgcv-pkg.tex [2642]
Chapter 24.
Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2643] [2644]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
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 []    \T1/pcr/m/n/10 sparse=FALSE,cluster=NULL,nthreads=NA,gc.level=1,use.chol
=FALSE,[] 
[2645]
Underfull \hbox (badness 1142) in paragraph at lines 175--179
\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 200--205
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2646] [2647] [2648] [2649]
Underfull \hbox (badness 10000) in paragraph at lines 368--375
[][][]\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 368--375
[][]\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 368--375
[][]\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 ,
[2650] [2651] [2652] [2653]
Underfull \hbox (badness 2922) in paragraph at lines 611--612
[]\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
[2654]
Underfull \hbox (badness 1158) in paragraph at lines 682--684
[]\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
[2655] [2656] [2657] [2658] [2659] [2660] [2661]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2662]
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 []\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)[] 
[2663] [2664] [2665] [2666] [2667] [2668]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1508--1508
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2669] [2670] [2671] [2672] [2673] [2674]
Underfull \hbox (badness 1052) in paragraph at lines 1879--1887
\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
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1900--1900
 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 
Underfull \hbox (badness 1728) in paragraph at lines 1907--1910
[]\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
[2675]
Underfull \hbox (badness 1142) in paragraph at lines 1920--1924
\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 1946--1951
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2676] [2677] [2678]
Underfull \hbox (badness 1043) in paragraph at lines 2106--2112
\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
[2679]
Underfull \hbox (badness 10000) in paragraph at lines 2233--2239
[][][]\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 2233--2239
[][]\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 2233--2239
[][]\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 ,
[2680] [2681]
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[2684] [2685] [2686] [2687] [2688] [2689] [2690]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2862--2862
 []         \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 2865--2865
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2691] [2692] [2693] [2694] [2695]
Underfull \hbox (badness 5189) in paragraph at lines 3180--3184
[]\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
[2696]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 3297--3297
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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[2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3867--3867
 []  \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)+[] 
[2707] [2708]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3982--3982
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
Underfull \hbox (badness 1142) in paragraph at lines 4013--4017
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2709] [2710] [2711]
Underfull \hbox (badness 5970) in paragraph at lines 4197--4203
[][][]\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 ,
[2712]
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[2714] [2715]
Underfull \hbox (badness 1577) in paragraph at lines 4462--4465
[]\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 4469--4470
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2716] [2717] [2718] [2719] [2720] [2721] [2722] [2723] [2724]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5058--5058
 []\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 5060--5060
 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
[2725]
Underfull \hbox (badness 1142) in paragraph at lines 5081--5085
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2726] [2727] [2728]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5248--5248
 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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[2730] [2731] [2732]
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[2734] [2735]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5637--5637
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5664--5664
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744]
Underfull \hbox (badness 1242) in paragraph at lines 6197--6198
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2745] [2746] [2747]
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 []\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 6333--6333
 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
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[2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759]
[2760] [2761] [2762] [2763] [2764]
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[2766]
Underfull \hbox (badness 10000) in paragraph at lines 7497--7500
[]\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 7497--7500
\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 7497--7500
\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 .
[2767]
Underfull \hbox (badness 10000) in paragraph at lines 7553--7556
[]\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 7553--7556
\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
[2768] [2769] [2770]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7777--7777
 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2771] [2772] [2773]
Underfull \hbox (badness 1629) in paragraph at lines 7929--7934
\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
[2774] [2775] [2776]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8130--8130
 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2777] [2778] [2779] [2780] [2781] [2782]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8533--8533
 []  \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[] 
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Underfull \hbox (badness 1205) in paragraph at lines 8571--8573
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\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 8577--8582
[]\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
[2784]
Underfull \hbox (badness 1205) in paragraph at lines 8661--8663
[]\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 8661--8663
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2785]
Underfull \hbox (badness 10000) in paragraph at lines 8730--8733
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\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,
[2786] [2787] [2788]
Underfull \hbox (badness 1253) in paragraph at lines 8860--8862
[]\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,
[2789] [2790] [2791]
Underfull \hbox (badness 1946) in paragraph at lines 9038--9045
[]\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 9038--9045
\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 9038--9045
\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
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[]\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:
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\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.
[2792]
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 []\T1/pcr/m/n/9 ## see also examples for gam.models, gam.vcomp, gamm and smoot
h.construct.re.smooth.spec 
[2793]
Underfull \hbox (badness 10000) in paragraph at lines 9125--9128
[]\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 ,
[2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] [2803] [2804]
[2805]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
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[]\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
[2806]
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\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 9923--9935
\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
[2807]
Underfull \hbox (badness 2401) in paragraph at lines 9940--9944
\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 9940--9944
\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 ,
[2808] [2809]
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Underfull \hbox (badness 6876) in paragraph at lines 10135--10141
[][][]\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
[2811]
Underfull \hbox (badness 10000) in paragraph at lines 10176--10177
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2812] [2813]
Underfull \hbox (badness 10000) in paragraph at lines 10294--10295
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2814]
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 []  \T1/pcr/m/n/9 sm <- smoothCon(s(x,bs="bs",m=m,k=k),data.frame(x),scale.pen
alty=FALSE)[[1]][] 
Underfull \hbox (badness 10000) in paragraph at lines 10399--10401
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
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\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
[2815] [2816] [2817]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2818]
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 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
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 []\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[] 
[2819]
Underfull \hbox (badness 7613) in paragraph at lines 10647--10650
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2820] [2821]
Underfull \hbox (badness 10000) in paragraph at lines 10756--10757
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2822] [2823] [2824] [2825]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10993--10993
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 11038--11040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2826] [2827]
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Underfull \hbox (badness 10000) in paragraph at lines 11197--11200
[]\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 11197--11200
\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 11197--11200
\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"
[2829] [2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11279--11279
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
Underfull \hbox (badness 10000) in paragraph at lines 11324--11330
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 11324--11330
\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-
[2831] [2832] [2833]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 11538--11538
 []\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...[] 
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 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 11541--11541
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 
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Overfull \hbox (90.78033pt too wide) in paragraph at lines 11622--11622
 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 
Overfull \hbox (85.38034pt too wide) in paragraph at lines 11628--11628
 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2836]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 11668--11669
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2837] [2838] [2839] [2840]
Underfull \hbox (badness 3396) in paragraph at lines 11929--11934
[][][]\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
[2841]
Underfull \hbox (badness 10000) in paragraph at lines 11974--11976
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2842] [2843] [2844] [2845]
Underfull \hbox (badness 10000) in paragraph at lines 12170--12173
[]\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 12170--12173
\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
Underfull \hbox (badness 10000) in paragraph at lines 12203--12207
[][][]\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 12203--12207
[][]\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 12203--12207
[][]\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 ,
[2846] [2847] [2848]
Underfull \hbox (badness 2158) in paragraph at lines 12363--12363
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2849]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 12438--12438
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2850] [2851]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 12572--12572
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2852] [2853] [2854]
Underfull \hbox (badness 4846) in paragraph at lines 12708--12711
[]\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
[2855] [2856] [2857] [2858] [2859]
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[2861] [2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 13678--13678
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2870] [2871] [2872] [2873] [2874]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 13968--13968
 []\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 13969--13969
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
[2875]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13981--13981
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2876] [2877]) (./nlme-pkg.tex [2878]
Chapter 25.
[2879]
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
[2880]
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
[2881] [2882] [2883] [2884] [2885]
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,[] 
[2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895]
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"),[] 
[2896]
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
[2897] [2898] [2899] [2900] [2901] [2902] [2903]
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 ,
[2904]
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
[2905] [2906] [2907] [2908] [2909]
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 ,
[2910]
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")[] 
[2911]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2912] [2913]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[2914]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2915] [2916] [2917] [2918] [2919] [2920] [2921] [2922]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933]
[2934]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4345--4345
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2946] [2947] [2948] [2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956]
[2957] [2958]
Underfull \hbox (badness 10000) in paragraph at lines 5155--5159
[][][]\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 ,
[2959] [2960] [2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 5472--5476
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5472--5476
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2964] [2965]
Underfull \hbox (badness 10000) in paragraph at lines 5587--5590
[][][]\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 ,
[2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
Underfull \hbox (badness 2799) in paragraph at lines 6093--6099
\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
[2975]
Underfull \hbox (badness 7133) in paragraph at lines 6154--6158
[]\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 ,
[2976]
Underfull \hbox (badness 2057) in paragraph at lines 6238--6249
[][][]\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 ,
[2977]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6306
[]\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 6336--6336
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2978] [2979] [2980] [2981]
Underfull \hbox (badness 7133) in paragraph at lines 6554--6558
[]\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 ,
[2982]
Underfull \hbox (badness 10000) in paragraph at lines 6653--6659
[][][]\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 ,
[2983]
Underfull \hbox (badness 10000) in paragraph at lines 6719--6721
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2984]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6749--6749
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2985] [2986] [2987]
Underfull \hbox (badness 10000) in paragraph at lines 6992--6999
[][][]\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 ,
[2988]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7009--7009
 []                \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
[2989] [2990] [2991]
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 ,
[2992] [2993] [2994]
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 1817) 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 
20 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 ,
[2995] [2996] [2997]
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
[2998] [2999] [3000] [3001] [3002] [3003]
Underfull \hbox (badness 1642) in paragraph at lines 8036--8058
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3004] [3005]
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
[3006] [3007] [3008] [3009] [3010]
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 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3011]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3012] [3013] [3014]
Underfull \hbox (badness 10000) in paragraph at lines 8722--8734
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9320
[][][]\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 9324--9324
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3024]
Underfull \hbox (badness 6300) in paragraph at lines 9406--9409
[]\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
[3025] [3026] [3027] [3028]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9675 ...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.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3029]
Underfull \hbox (badness 10000) in paragraph at lines 9695--9698
[]\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 9739--9742
[]\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 9739--9742
\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
[3030] [3031] [3032]
Underfull \hbox (badness 2435) in paragraph at lines 9913--9918
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 7291) in paragraph at lines 10203--10205
[]\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
[3038] [3039] [3040]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3041]
Underfull \hbox (badness 1596) in paragraph at lines 10448--10474
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3042] [3043] [3044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3045] [3046]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
[3047]
Underfull \hbox (badness 10000) in paragraph at lines 10823--10825
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10835--10838
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10858--10858
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058]
[3059] [3060] [3061] [3062]
Underfull \hbox (badness 6268) in paragraph at lines 11890--11900
[][][]\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 ,
[3063] [3064] [3065] [3066]
Underfull \hbox (badness 10000) in paragraph at lines 12151--12157
[][][]\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 ,
[3067] [3068] [3069] [3070] [3071]
Underfull \hbox (badness 6876) in paragraph at lines 12473--12475
[]\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
[3072] [3073]
Underfull \hbox (badness 2452) in paragraph at lines 12629--12636
[][][]\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 ,
[3074]
Underfull \hbox (badness 10000) in paragraph at lines 12694--12700
[][][]\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 ,
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
[3086] [3087] [3088] [3089]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13646--13646
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
Underfull \hbox (badness 10000) in paragraph at lines 13673--13676
[]\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
[3090]
Underfull \hbox (badness 6016) in paragraph at lines 13701--13704
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13701--13704
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13708--13711
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13716--13723
[]\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 13716--13723
\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
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13773--13773
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13780--13783
[]\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 13780--13783
\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
[3092]
Underfull \hbox (badness 4582) in paragraph at lines 13808--13811
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13808--13811
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13812--13815
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3093]
Underfull \hbox (badness 10000) in paragraph at lines 13888--13891
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13913--13920
\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 ,
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 13982--13984
[][][]\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 ,
[3095] [3096] [3097]
Underfull \hbox (badness 1540) in paragraph at lines 14197--14202
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
[3098]
Underfull \hbox (badness 1215) in paragraph at lines 14244--14246
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3099] [3100] [3101] [3102] [3103]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14488--14488
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]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.15144 ...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.15144 ...Extract Random Effects}{random.effects}
                                                   [3113] [3114] [3115]
[3116] [3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1009) in paragraph at lines 15801--15810
\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
[3123] [3124] [3125]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15948--15948
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3126] [3127] [3128] [3129]
Underfull \hbox (badness 10000) in paragraph at lines 16226--16244
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16226--16244
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3130]
Underfull \hbox (badness 10000) in paragraph at lines 16283--16289
[][][]\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 ,
[3131]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16314--16314
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3132] [3133] [3134] [3135] [3136] [3137] [3138]
Underfull \hbox (badness 1728) in paragraph at lines 16798--16801
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3139] [3140] [3141] [3142] [3143]
Underfull \hbox (badness 1867) in paragraph at lines 17131--17140
\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 17131--17140
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17131--17140
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3144]
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17195--17203
\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 ,
[3145] [3146] [3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 17442--17449
[][][]\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 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156]
Underfull \hbox (badness 10000) in paragraph at lines 17972--17982
[][][]\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 17972--17982
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18010--18015
\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
[3157]
Underfull \hbox (badness 3579) in paragraph at lines 18074--18079
\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
[3158]
Underfull \hbox (badness 3579) in paragraph at lines 18137--18142
\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
[3159]
Underfull \hbox (badness 1577) in paragraph at lines 18198--18200
[]\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 18200--18205
\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
[3160]
Underfull \hbox (badness 3579) in paragraph at lines 18263--18268
\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
[3161]
Underfull \hbox (badness 10000) in paragraph at lines 18296--18305
[][][]\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 18296--18305
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18335--18340
\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
[3162] [3163] [3164]
Underfull \hbox (badness 1009) in paragraph at lines 18484--18493
\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
[3165] [3166]
Underfull \hbox (badness 1009) in paragraph at lines 18618--18627
\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
[3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174]) (./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}
                                                   [3175]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3176] [3177] [3178]
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,[] 
[3179]
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)[] 
[3180]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3181]
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,[] 
[3182]) (./rpart-pkg.tex
Chapter 27.
[3183] [3184] [3185] [3186]
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, ...)[] 
[3187]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3188] [3189] [3190]
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
[3191] [3192]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3193]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3194]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3195]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3196] [3197] [3198]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3199]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3200]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\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 1286--1286
 []\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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3201] [3202] [3203] [3204] [3205] [3206]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3207] [3208]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3209] [3210] [3211]) (./spatial-pkg.tex [3212]
Chapter 28.
[3213] [3214] [3215] [3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3219] [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
[3230] [3231]) (./survival-pkg.tex [3232]
Chapter 29.
[3233] [3234]
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.[] 
[3235]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 226--226
 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... 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.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3236] [3237]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
 []\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 366--366
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3238]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3239] [3240] [3241]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 598--598
 []\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 599--599
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3242] [3243]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 742--742
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3244] [3245] [3246]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 972--972
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3247]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1040 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3248] [3249] [3250]
[3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1854--1854
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3259] [3260] [3261] [3262]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2101--2101
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3263] [3264] [3265] [3266]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2418--2418
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3267]
Underfull \hbox (badness 1389) in paragraph at lines 2431--2433
[]\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
Underfull \hbox (badness 1048) in paragraph at lines 2474--2476
[]\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
[3268]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2545--2545
 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2551--2551
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3269] [3270] [3271] [3272] [3273]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2798--2798
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3274] [3275] [3276]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3027--3027
 []                    \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 )))[] 
[3277] [3278] [3279] [3280]
Underfull \vbox (badness 10000) has occurred while \output is active [3281]
[3282] [3283]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3436--3436
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3284] [3285]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3625--3625
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3286] [3287]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3739--3739
 []\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[] 
[3288]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3289] [3290] [3291]
Underfull \hbox (badness 1852) in paragraph at lines 3977--3979
[]\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
[3292] [3293]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4110--4110
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3294] [3295]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3296]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4371--4371
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3297]
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 []\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 4394--4394
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3298] [3299]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4539--4539
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3300] [3301] [3302] [3303]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4867--4867
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
[3304]
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4879--4884
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3305] [3306]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5052--5052
 []\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 5053--5053
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3307] [3308] [3309] [3310] [3311] [3312] [3313]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 5557--5557
 []    \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 ),[] 
[3314] [3315] [3316] [3317]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3318]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3319]
Underfull \hbox (badness 1038) in paragraph at lines 5969--5975
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
Underfull \hbox (badness 3000) in paragraph at lines 5991--5993
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3320]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 6021--6021
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3321]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6107--6107
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3322] [3323] [3324]
Underfull \hbox (badness 10000) in paragraph at lines 6314--6319
[][][]\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 ,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6335--6335
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3325] [3326]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3327] [3328]
Underfull \hbox (badness 6332) in paragraph at lines 6642--6647
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3329] [3330]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3331] [3332] [3333]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3334]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3335] [3336]
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\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 .
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\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 ,
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\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
[3337]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3338] [3339] [3340]
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 []                 \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 )[] 
[3341] [3342]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \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 )[] 
[3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3347] [3348] [3349] [3350] [3351]) [3352] (./fullrefman.ind [3353] [3354]
[3355] [3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365]
[3366] [3367] [3368] [3369] [3370] [3371] [3372]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
[3373]
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3374] [3375] [3376] [3377] [3378]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3379]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
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[3388]
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[3389]
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Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
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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>
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[7] [8] [9] [10] Chapter 3 [11] [12]
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 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[13] [14] [15] [16] Chapter 4 [17]
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[][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small
tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o
r
[18] Chapter 5 [19] Chapter 6 [20] [21] [22] [23]
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[24] [25] [26] [27] Chapter 7 [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
[33] [34] Appendix A [35] [36]
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 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d
isable-cpp[] 
[37] [38] [39] [40] [41] [42] [43] Appendix B [44] [45] [46] [47] [48]
Appendix C [49] [50] [51] [52] [53]
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[]@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. %
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@textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A
[]rn-Helge
[54] [55]
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 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[56] [57] [58] [59]
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[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[60] [61] [62] [63] Appendix D [64] [65] [66] (Function and variable index)
[67] (Concept index) [68] (Environment variable index) [69] [70] )
(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
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Output written on R-admin.pdf (73 pages, 448601 bytes).
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This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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entering extended mode
(/builddir/build/BUILD/R-3.3.0/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
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}] [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] Chapter 3 [11]
[12]
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 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[13] [14] [15] [16] Chapter 4 [17]
Underfull \hbox (badness 10000) in paragraph at lines 1713--1717
[][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small
tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o
r
[18] Chapter 5 [19] Chapter 6 [20] [21] [22] [23]
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[24] [25] [26] [27] Chapter 7 [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
[33] [34] Appendix A [35] [36]
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 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d
isable-cpp[] 
[37] [38] [39] [40] [41] [42] [43] Appendix B [44] [45] [46] [47] [48]
Appendix C [49] [50] [51] [52] [53]
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[]@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. %
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@textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A
[]rn-Helge
[54] [55]
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 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[56] [57] [58] [59]
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[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[60] [61] [62] [63] Appendix D [64] [65] [66] (Function and variable index)
[67] (./R-admin.vrs) (Concept index) [68] (./R-admin.cps)
(Environment variable index) [69] (./R-admin.ens) [70] )
(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
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</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
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Output written on R-admin.pdf (75 pages, 495350 bytes).
Transcript written on R-admin.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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entering extended mode
(/builddir/build/BUILD/R-3.3.0/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
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(./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] Chapter 3 [11]
[12]
Underfull \hbox (badness 7685) in paragraph at lines 1183--1187
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[13] [14] [15] [16] Chapter 4 [17]
Underfull \hbox (badness 10000) in paragraph at lines 1713--1717
[][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small
tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o
r
[18] Chapter 5 [19] Chapter 6 [20] [21] [22] [23]
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[24] [25] [26] [27] Chapter 7 [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
[33] [34] Appendix A [35] [36]
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 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d
isable-cpp[] 
[37] [38] [39] [40] [41] [42] [43] Appendix B [44] [45] [46] [47] [48]
Appendix C [49] [50] [51] [52] [53]
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[]@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. %
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@textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A
[]rn-Helge
[54] [55]
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 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 5195--5198
[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[60] [61] [62] [63] Appendix D [64] [65] [66] (Function and variable index)
[67] (./R-admin.vrs) (Concept index) [68] (./R-admin.cps)
(Environment variable index) [69] (./R-admin.ens) [70] )
(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
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Output written on R-admin.pdf (75 pages, 495350 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)
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entering extended mode
(/builddir/build/BUILD/R-3.3.0/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)
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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
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</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/
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Output written on R-data.pdf (33 pages, 265090 bytes).
Transcript written on R-data.log.
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entering extended mode
(/builddir/build/BUILD/R-3.3.0/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)
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 [][]@textbf dataframes2xls[][]| 
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 [][]@textbf RPostgreSQL[][]| 
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 [][]@textbf xlsReadWrite[][]| 
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
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fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (35 pages, 304299 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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entering extended mode
(/builddir/build/BUILD/R-3.3.0/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)
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 [][]@textbf dataframes2xls[][]| 
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 [][]@textbf RPostgreSQL[][]| 
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 [][]@textbf xlsReadWrite[][]| 
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
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sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
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(Acknowledgements)
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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] )
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
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[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] [51] [52] [53] [54]
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[71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82]
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(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
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[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] [51] [52] [53] [54]
[55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67]
[68]
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[71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82]
Chapter 4 [83] [84] [85] [86] [87]
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[94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105]
[106] [107] [108] [109]
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[163] [164] (Function and variable index) [165] (./R-exts.vrs [166] [167])
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(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
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[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
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[40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54]
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[71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82]
Chapter 4 [83] [84] [85] [86] [87]
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[106] [107] [108] [109]
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[131] [132] Chapter 6 [133] [134] [135] [136] [137] [138] [139] [140] [141]
[142] [143] [144] [145] Warning: unbalanced parentheses in @def... [146]
[147] [148] [149]
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[150] Chapter 7 [151] [152] Chapter 8 [153] [154] [155]
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(Acknowledgements) Chapter 1 [1] [2] [3] [4] [5]
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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]
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pp model/*/*.cpp model/*/*/*.cpp)[] 
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a07models.o $(SOURCES:.cpp=.o)[] 
[25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]
[40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54]
[55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67]
[68]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[69] [70]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82]
Chapter 4 [83] [84] [85] [86] [87]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[88] [89] [90] [91]
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odr_violation=0'[] 
[92]
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exttt -
[93]
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[94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105]
[106] [107] [108] [109]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[110] [111] [112] [113] [114] [115] [116] [117] [118]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130]
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[131] [132] Chapter 6 [133] [134] [135] [136] [137] [138] [139] [140] [141]
[142] [143] [144] [145] Warning: unbalanced parentheses in @def... [146]
[147] [148] [149]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
[150] Chapter 7 [151] [152] Chapter 8 [153] [154] [155]
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tatic libR[] 
[156]
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nst char *);[] 
[157] [158] [159] [160] [161] [162]
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[163] [164] (Function and variable index) [165] (./R-exts.vrs [166] [167])
(Concept index) [168] (./R-exts.cps [169]) [170] )
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi
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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]
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[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] )
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(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]
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[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] )
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}] [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]
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[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] )
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[13] [14] [15] [16] [17] [18] [19] [20] Chapter 2 [21] [22] [23] [24] [25]
Chapter 3 [26] [27] Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] [32]
[33] [34] [35] [36] [37] [38] [39] [40] [41] Chapter 7 [42] [43] Chapter 8
[44] [45]
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[46] [47] [48] [49] Chapter 9 [50] [51] Chapter 10 [52] Chapter 11 [53]
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[57] [58] )
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[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18] [19] [20] Chapter 2 [21] [22] [23] [24] [25] Chapter 3 [26] [27]
Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] Chapter 7 [42] [43] Chapter 8 [44] [45]
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[46] [47] [48] [49] Chapter 9 [50] [51] Chapter 10 [52] Chapter 11 [53]
Chapter 12 [54] [55] (Function and variable index) [56] (./R-ints.vrs [57])
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[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18] [19] [20] Chapter 2 [21] [22] [23] [24] [25] Chapter 3 [26] [27]
Chapter 4 [28] [29] Chapter 5 [30] Chapter 6 [31] [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] Chapter 7 [42] [43] Chapter 8 [44] [45]
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[46] [47] [48] [49] Chapter 9 [50] [51] Chapter 10 [52] Chapter 11 [53]
Chapter 12 [54] [55] (Function and variable index) [56] (./R-ints.vrs [57])
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[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]
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[]@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
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[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]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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[46] [47] [48] [49] [50] (Function and Variable Index) [51] (./R-lang.vrs
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[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]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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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
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-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, 376178 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-3.3.0/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 4344--4346
[]@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, 376178 bytes).
Transcript written on R-lang.log.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc'
+ make MAKEINFO=texi2any info
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/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.GAkE0V
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm
++ dirname /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm
+ cd R-3.3.0
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.3.0-3.el7.arm install install-info
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/m4'
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make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/tools'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tools'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc'
installing doc ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/man/man1
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/html'
installing doc/html ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/html
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make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
installing doc/manual ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/manual
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/manual/images
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make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/etc'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/etc
installing etc ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/etc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/share'
installing share ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/dictionaries
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/encodings
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/java
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/licenses
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/make
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/Rd
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/Rd/macros
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/sh
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/texmf
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/texmf/bibtex/bib
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/texmf/bibtex/bst
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/texmf/tex/latex
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/share'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/bin
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/bin
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/scripts'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/include/R
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include/R_ext'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/include/R/R_ext
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include/R_ext'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/lib
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/blas'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/tre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/tre'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/xdr'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/xdr'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/extra/intl'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra/intl'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/appl'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/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-3.3.0-3.el7.arm/usr/lib/pkgconfig
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/main'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/bin/exec
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/modules
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/modules/X11'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules/X11'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/library'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
mkdir -p -- /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/info
/usr/bin/install -c -m 644 "./dir" "/builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/info"
installing R info pages ...
updating '/usr/share/info/dir' ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.3.0-3.el7.arm install-pdf
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/doc/manual'
+ rm -f /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/info/dir
+ rm -f /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/info/dir.old
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0
+ install -p CAPABILITIES /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0
+ cd src/nmath/standalone
+ make install DESTDIR=/builddir/build/BUILDROOT/R-3.3.0-3.el7.arm
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/include'
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/etc/ld.so.conf.d
+ echo /usr/lib/R/lib
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/library
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/rpm/macros.d/
+ install -m0644 /builddir/build/SOURCES/macros.R /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/rpm/macros.d/
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/rpm/
+ install -m0755 /builddir/build/SOURCES/R-make-search-index.sh /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/rpm/
+ touch -r README /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/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-3.3.0-3.el7.arm/usr/bin/R
+ sed -i 's|\..\/\..|/usr/lib/R|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/html/packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/bkde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/bkde2D.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/bkfe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/dpih.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/dpik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/dpill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/KernSmooth/html/locpoly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Aids2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Boston.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Cars93.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Cushings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/DDT.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/GAGurine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Insurance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/MASS-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/OME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Pima.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Rabbit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Rubber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/SP500.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Sitka.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Sitka89.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Skye.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/Traffic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/UScereal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/UScrime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/VA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/abbey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/accdeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/addterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/anorexia.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/anova.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/area.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/bacteria.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/bandwidth.nrd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/bcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/beav1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/beav2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/biopsy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/birthwt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/boxcox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cabbages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/caith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cement.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/chem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/con2tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/contr.sdif.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/coop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/corresp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cov.rob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cov.trob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/cpus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/crabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/deaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/denumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/dose.p.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/drivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/dropterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/eagles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/epil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/eqscplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/farms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/fgl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/fitdistr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/forbes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/fractions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/galaxies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/gamma.dispersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/gamma.shape.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/gehan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/genotype.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/geyser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/gilgais.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/ginv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/glm.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/glm.nb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/hills.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/hist.scott.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/housing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/huber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/hubers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/immer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/isoMDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/kde2d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/ldahist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/leuk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/lm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/lm.ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/loglm1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/logtrans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/mammals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/mcycle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/menarche.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/michelson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/minn38.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/motors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/mvrnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/negative.binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/newcomb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/nlschools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/npr1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/painters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/pairs.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/parcoord.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/petrol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/phones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/plot.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/plot.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/plot.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/polr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/predict.glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/predict.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/predict.lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/predict.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/predict.qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/profile.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/quine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/rational.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/renumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/rms.curv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/rnegbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/road.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/rotifer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/sammon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/ships.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/shoes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/shrimp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/shuttle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/snails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/stdres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/steam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/stepAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/stormer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/studres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/summary.loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/summary.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/summary.rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/survey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/synth.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/theta.md.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/topo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/truehist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/ucv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/Schur.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/Xtrct-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/abIndex-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/all.equal-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/atomicVector-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/band.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/bdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/boolean-matprod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/cBind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/chol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/colSums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/condest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ddenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ddiMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/denseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dgCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dgRMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dgTMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dgeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/diagU2N.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/diagonalMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dpoMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/drop0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dsCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dsRMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dsparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dtCMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dtRMatrix-class-def.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dtpMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dtrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/expm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/externalFormats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/facmul.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/forceSymmetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/formatSparseM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/generalMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/graph2T.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/image-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/indMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/index-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/invPerm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/is.na-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/is.null.DN.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/isSymmetric-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/isTriangular.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/kronecker-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ldenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ldiMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/lgeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/lsparseMatrix-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/lsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ltrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/lu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/matrix-products.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/nMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ndenseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/nearPD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ngeMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/nnzero.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/nsparseMatrix-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/nsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/ntrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/number-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/pMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/printSpMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/qr-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/rankMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/rcond.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/rep2abI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/replValue-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/rleDiff-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/rsparsematrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/solve-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/spMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparse.model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseLU-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseQR-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseVector-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/sparseVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/symmetricMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/symmpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/triangularMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/uniqTsparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/unpack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/unused-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/updown.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Arithmetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/AsIs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Bessel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/CallExternal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Comparison.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Constants.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Cstack_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/DateTimeClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Dates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Encoding.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/EnvVar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Extract.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Extract.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Extremes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Foreign-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Hyperbolic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ISOdatetime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/InternalMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/La_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Last.value.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Log.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Logic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/LongVectors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/MathFun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Memory-limits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Memory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/NA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/NULL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/NumericConstants.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Ops.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Paren.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Platform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Primitive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Quotes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Random-user.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Random.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/RdUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Recall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Reserved.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Rhome.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Round.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Signals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Special.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Startup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Syntax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.getenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.getpid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.glob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.localeconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.readlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.setFileTime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.setenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Sys.which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Trig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/UseMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Vectorize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/abbreviate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/agrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/all.equal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/all.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/allnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/any.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/aperm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/append.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/apply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/args.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/as.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/as.POSIXlt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/as.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/as.environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/as.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/assign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/assignOps.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/attach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/attr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/attributes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/autoload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/backsolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/base-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/base-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/base-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/base-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/basename.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/bincode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/bindenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/bitwise.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/body.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/bquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/browser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/browserText.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/builtins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/by.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/callCC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/cat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/cbind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/char.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/character.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/charmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/chartr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/chkDots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/chol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/chol2inv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/col.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/colSums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/colnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/commandArgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/comment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/complex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/conditions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/conflicts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/connections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/contributors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/copyright.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/crossprod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/cumsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/curlGetHeaders.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/cut.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/cut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/data.class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/data.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dataframeHelpers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dcf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/debug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/delayedAssign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/deparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/deparseOpts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/det.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/detach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/diff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/difftime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dimnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/do.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dontCheck.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/double.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dput.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/drop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/droplevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dump.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/duplicated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/dynload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/eapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/eigen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/encodeString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/eval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/exists.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/expand.grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/expression.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/extSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/file.access.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/file.choose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/file.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/file.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/file.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/files2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/find.package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/findInterval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/forceAndCall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/formals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/format.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/format.pval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/formatDL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/formatc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/funprog.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gctorture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/getCallingDLL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/getDLLRegisteredRoutines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/getLoadedDLLs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/getNativeSymbolInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/getwd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/grepRaw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/grouping.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/gzcon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/hexmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/iconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/icuSetCollate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/identical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/identity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ifelse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/integer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/invisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.finite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.language.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.recursive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.single.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/is.unsorted.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/isR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/isS4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/isSymmetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/jitter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/kappa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/kronecker.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/l10n_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/labels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/lapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/lazyload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/lengths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/levels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/libPaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/libcurlVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/library.dynam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/library.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/license.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/list.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/list2env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/locales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/logical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/lower.tri.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/make.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/make.unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/mapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/margin.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/mat.or.vec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/match.arg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/match.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/match.fun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/match.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/matmult.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/maxCol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/memCompress.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/memory.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/merge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/message.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/missing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/mode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/nargs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/nchar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/nlevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/noquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/normalizePath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/notyet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/nrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-dblcolon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-hooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-reflect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/ns-topenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/numeric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/numeric_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/octmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/on.exit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/order.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/parse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/paste.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/path.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/pcre_config.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/pmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/polyroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/pos.to.env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/print.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/print.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/prmatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/proc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/prod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/prop.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/pushBack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/qr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/qraux.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/quit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/range.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/raw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rawConnection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rawConversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readBin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readChar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readRDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readRenviron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/readline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/reg.finalizer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/regex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/regmatches.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/replace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/round.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/row.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/row.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/rowsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sample.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/save.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/scan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/seek.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/seq.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/seq.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/seq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sequence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/serialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/setTimeLimit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/shQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/showConnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/slice.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/slotOp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/socketSelect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/solve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sort.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/split.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sprintf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/srcfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/standardGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/startsWith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/stop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/stopifnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strptime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strsplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strtoi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strtrim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/structure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/strwrap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/subset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/substitute.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/substr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/svd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sweep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/switch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sys.parent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/sys.source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/system.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/system.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/system.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/system2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/t.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/tabulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/tapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/taskCallback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/taskCallbackManager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/taskCallbackNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/tempfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/textconnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/tilde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/timezones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/toString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/trace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/traceback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/tracemem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/transform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/trimws.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/try.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/typeof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/unlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/unlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/unname.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/userhooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/utf8Conversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/validUTF8.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/vector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/warning.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/warnings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/weekday.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/which.min.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/with.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/withVisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/write.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/writeLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/xtfrm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/zMachine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/zScript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/zapsmall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/zpackages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/zutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/EEF.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/Imp.Estimates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/abc.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/acme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/aids.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/aircondit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/amis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/beaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/bigcity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/boot-practicals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/boot.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/boot.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/brambles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/breslow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/calcium.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cane.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/capability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/catsM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cav.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cd4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cd4.nested.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/censboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/channing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/claridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cloth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/co.transfer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/coal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/corr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cum3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/cv.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/darwin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/dogs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/downs.bc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/ducks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/empinf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/envelope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/exp.tilt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/fir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/freq.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/frets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/glm.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/glm.diag.plots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/gravity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/hirose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/imp.weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/inv.logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/islay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/jack.after.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/k3.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/linear.approx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/lines.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/manaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/motor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/neuro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/nitrofen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/nodal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/norm.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/nuclear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/paulsen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/plot.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/poisons.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/polar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/print.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/print.bootci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/print.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/print.simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/remission.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/saddle.distn.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/saddle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/salinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/simplex.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/smooth.f.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/sunspot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/survival.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/tau.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/tilt.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/tsboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/tuna.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/urine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/var.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/boot/html/wool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/SOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/batchSOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/condense.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/knn.cv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/knn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/knn1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/lvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/lvq2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/lvq3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/lvqinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/lvqtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/multiedit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/olvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/reduce.nn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/class/html/somgrid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/agnes.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/agriculture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/bannerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/chorSub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/clara.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/clusGap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/clusplot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/clusplot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/cluster-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/coef.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/daisy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/dissimilarity.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/ellipsoidhull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/fanny.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/flower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/lower.to.upper.tri.inds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/mona.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/pam.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/partition.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/plantTraits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/plot.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/plot.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/plot.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/plot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/pltree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/pluton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/predict.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.dissimilarity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/print.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/ruspini.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/silhouette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/sizeDiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/summary.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/summary.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/summary.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/summary.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/summary.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/twins.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/volume.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/votes.repub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/cluster/html/xclara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/codetools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/codetools/html/checkUsage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/codetools/html/codetools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/codetools/html/findGlobals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/codetools/html/showTree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/compiler/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/compiler/html/compile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/AirPassengers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/BJsales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/BOD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/ChickWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/DNase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/EuStockMarkets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Formaldehyde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/HairEyeColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Harman23.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Harman74.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Indometh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/InsectSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/JohnsonJohnson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/LakeHuron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/LifeCycleSavings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Loblolly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Nile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Orange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/OrchardSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/PlantGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Puromycin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Theoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/Titanic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/ToothGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/UCBAdmissions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/UKDriverDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/UKLungDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/UKgas.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/USAccDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/USArrests.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/USJudgeRatings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/USPersonalExpenditure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/VADeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/WWWusage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/WorldPhones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/ability.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/airmiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/airquality.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/anscombe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/attenu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/attitude.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/austres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/beavers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/cars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/chickwts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/co2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/crimtab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/datasets-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/discoveries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/esoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/euro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/eurodist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/faithful.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/freeny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/infert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/iris.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/islands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/lh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/longley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/lynx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/morley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/mtcars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/nhtemp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/nottem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/occupationalStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/precip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/presidents.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/pressure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/quakes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/randu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/rivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/rock.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/stackloss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/state.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/sunspot.month.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/sunspot.year.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/sunspots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/swiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/treering.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/trees.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/uspop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/volcano.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/warpbreaks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/women.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/datasets/html/zCO2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/lookup.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.S.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.epiinfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.mtp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.octave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.spss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.ssd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.systat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/read.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/write.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/write.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/write.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/foreign/html/write.foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/Devices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/Hershey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/Japanese.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/Type1Font.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/adjustcolor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/as.graphicsAnnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/as.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/axisTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/boxplot.stats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/cairo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/check.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/chull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/cm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/col2rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/colorRamp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/contourLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/convertColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/densCols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.capture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.flush.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/dev2bitmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/devAskNewPage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/embedFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/extendrange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/getGraphicsEvent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/grDevices-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/grSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/gray.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/gray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/hcl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/make.rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/n2mfrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/nclass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/palette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/palettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/pdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/pdf.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/pictex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/plotmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/png.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/postscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/postscriptFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/pretty.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/ps.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/quartz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/quartzFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/recordGraphics.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/recordplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/rgb2hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/savePlot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/trans3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/x11.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/x11Fonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/xfig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/xy.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/xyTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grDevices/html/xyz.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/abline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/arrows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/assocplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/axTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/axis.POSIXct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/barplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/box.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/boxplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/boxplot.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/bxp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/cdplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/convertXY.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/coplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/dotchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/filled.contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/fourfoldplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/graphics-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/graphics-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/hist.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/hist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/identify.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/image.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/matplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/mosaicplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/mtext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/panel.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/par.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/persp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/pie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.design.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.xy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plothistogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/polypath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/rasterImage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/rug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/screen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/spineplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/stars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/stem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/stripchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/strwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/sunflowerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/symbols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/title.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/units.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/zAxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/Grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/absolute.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/arrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/calcStringMetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/current.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/dataViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/depth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/drawDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/editDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/explode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/gEdit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/gPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/getNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/gpar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.DLapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.add.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.bezier.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.cap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.circle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.copy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.delay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.display.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.draw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.grab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.grill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.grob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.move.to.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.newpage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.pack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.place.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.plot.and.legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.record.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.refresh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.remove.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.reorder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.roundrect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.set.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.show.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.show.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.xaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grid.yaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grobName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grobWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/grobX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/legendGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/makeContent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/plotViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/resolveRasterSize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/showGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/showViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/stringWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/unit.c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/unit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/unit.length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/unit.pmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/unit.rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/valid.just.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/validDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/viewports.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/vpPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/widthDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/xDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/grid/html/xsplinePoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/Lattice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/Rows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/axis.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/banking.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/barchart.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/barley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/draw.colorkey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/draw.key.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/environmental.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/ethanol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/lattice.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/latticeParseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/level.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/llines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/lset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/make.groups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/oneway.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/packet.panel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.barchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.bwplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.densityplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.dotplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.number.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.qqmathline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.stripplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.superpose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.violin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/panel.xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/prepanel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/prepanel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/print.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/qq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/rfs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/shingles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/simpleKey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/simpleTheme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/singer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/splom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/strip.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/tmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/trellis.device.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/trellis.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/trellis.par.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/update.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/utilities.3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/lattice/html/xyplot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/BasicClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/Classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/Documentation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/EmptyMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/EnvironmentClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/GenericFunctions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/LanguageClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/LinearMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/MethodDefinition-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/MethodSupport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/MethodWithNext-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/Methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/MethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/MethodsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/NextMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/ObjectsWithPackage-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/RClassUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/RMethodUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/S3Part.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/S4groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/SClassExtension-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/StructureClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/TraceClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/as.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/callGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/canCoerce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/cbind2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/className.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/classRepresentation-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/classesToAM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/dotsMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/evalSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/findClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/findMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/fixPrevious.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/genericFunction-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/getClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/getMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/getPackageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/hasArg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/implicitGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/inheritedSlotNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/initialize-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/is.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/isSealedMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/languageEl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/localRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/method.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/methodUtilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/methods-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/methods-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/methods-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/new.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/nonStructure-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/promptClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/promptMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/refClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/representation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/selectSuperClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setClassUnion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setLoadActions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setOldClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/setSClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/showMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/signature-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/slot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/stdRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/substituteDirect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/testInheritedMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/validObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/methods/html/zBasicFunsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.cr.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Predict.matrix.soap.film.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Rrank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/Tweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/anova.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/bam.update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/bandchol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/bug.reports.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/cSplineDes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/choose.k.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/columb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/concurvity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/exclude.too.far.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/extract.lme.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/family.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/fix.family.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/fixDependence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/formXtViX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/formula.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/fs.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/full.score.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.check.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.convergence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.fit3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.models.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.selection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.side.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam.vcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gam2objective.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gamObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gamSim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gamm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/gaulss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/get.var.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/in.out.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/inSide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/influence.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/initial.sp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/interpret.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/jagam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/ldTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/linear.functional.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/logLik.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/ls.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/magic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/magic.post.proc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mgcv-FAQ.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mgcv-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mgcv-parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/missing.data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/model.matrix.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mono.con.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/new.name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/notExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/notExp2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/null.space.dimension.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/ocat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/pcls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/pdIdnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/pdTens.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/pen.edf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/place.knots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/plot.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/polys.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/predict.bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/predict.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/print.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/qq.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/rTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/residuals.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/rig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/rmvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/s.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/scat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/sdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/single.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/slanczos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.bs.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.gp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.re.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.so.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.sos.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.t2.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smooth.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/smoothCon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/sp.vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/spasm.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/step.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/summary.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/t2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/te.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/tensor.prod.model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/trichol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/uniquecombs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/vcov.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/vis.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/ziP.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/ziplss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ACF.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ACF.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Alfalfa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Assay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/BodyWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Cefamandole.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Covariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Covariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dialyzer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dim.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dim.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dim.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Earthquake.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Extract.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Fatigue.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Gasoline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Glucose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Glucose2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Gun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/IGF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Initialize.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/LDEsysMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Machines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/MathAchSchool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/MathAchieve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Meat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Milk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Names.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Names.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Names.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Names.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Nitrendipene.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Orthodont.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Ovary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Oxboys.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Oxide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/PBG.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Phenobarb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Pixel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Quinidine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Rail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/RatPupWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Relaxin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Remifentanil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Soybean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Spruce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Tetracycline1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Tetracycline2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/VarCorr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Variogram.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Wafer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Wheat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Wheat2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/allCoef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/anova.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/anova.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/as.matrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/as.matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/as.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/asOneFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/asTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/balancedGrouped.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/bdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/coef.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/collapse.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/collapse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/comparePred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corARMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corCAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corFactor.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corMatrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corMatrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/corSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ergoStool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fdHess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fitted.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fixed.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/fixef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/formula.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/formula.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/formula.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getCovariate.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getCovariate.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getCovariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getCovariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getCovariateFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getData.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getData.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getData.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroups.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getGroupsFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getResponse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getResponseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/getVarCov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gls-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/glsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/glsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gnlsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gnlsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/gsummary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/intervals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/intervals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/intervals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/isBalanced.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/isInitialized.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lmList.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lme.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lme.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logDet.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logDet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logDet.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logDet.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/logLik.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/model.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/needUpdate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/needUpdate.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlme.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/nlsList.selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pairs.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pairs.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pairs.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdConstruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdConstruct.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdDiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdFactor.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdLogChol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pdSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/phenoModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.nffGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.nfnGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.nmGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/plot.ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/pooledSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/predict.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/predict.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/predict.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/predict.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/predict.nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/print.summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/print.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/qqnorm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/qqnorm.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/quinModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/recalc.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/recalc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/recalc.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/recalc.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/recalc.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/residuals.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/simulate.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/solve.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/solve.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/splitFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/summary.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/update.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/update.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varComb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varConstPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varFixed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varWeights.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varWeights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/varWeights.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/class.ind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/nnet.Hess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/predict.nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/which.is.max.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/RngStream.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/children.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/clusterApply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/detectCores.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/makeCluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/mcaffinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/mcfork.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/mclapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/mcparallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/parallel-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/pvec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/parallel/html/splitIndices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/car.test.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/car90.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/cu.summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/kyphosis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/labels.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/meanvar.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/na.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/path.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/plot.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/plotcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/post.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/predict.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/print.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/printcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/prune.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/residuals.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rpart-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rpart.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rpart.exp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rpart.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/rsq.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/snip.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/solder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/stagec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/summary.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/text.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/xpred.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/Kaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/Kenvl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/Kfn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/Psim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/SSI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/Strauss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/anova.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/correlogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/expcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/ppgetregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/ppinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/pplik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/ppregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/predict.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/prmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/semat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/surf.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/surf.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/trls.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/trmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/spatial/html/variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/asVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/backSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/interpSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/ns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/periodicSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/polySpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/predict.bSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/predict.bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/splineDesign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/splineKnots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/splineOrder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/splines-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/splines/html/xyVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/AIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ARMAacf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ARMAtoMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Cauchy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Chisquare.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Exponential.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Fdist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/GammaDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Geometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Hypergeometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/IQR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/KalmanLike.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Logistic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Lognormal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/NLSstAsymptotic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/NLSstClosestX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/NLSstLfAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/NLSstRtAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/NegBinomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Normal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Poisson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSasymp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSasympOff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSasympOrig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSbiexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSfol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSfpl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSgompertz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSlogis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSmicmen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SSweibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/SignRank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/StructTS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/TDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Tukey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/TukeyHSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Uniform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Weibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/Wilcoxon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/acf2AR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/add1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/addmargins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/aggregate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/alias.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/anova.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/anova.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/anova.mlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ansari.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/approxfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ar.ols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/arima.sim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/arima0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/as.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/asOneSidedFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/bandwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/bartlett.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/binom.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/biplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/biplot.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/birthday.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/box.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cancor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/case.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/checkMFClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/chisq.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cmdscale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/complete.cases.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/constrOptim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/contrasts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/convolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cophenetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cor.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cov.wt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cpgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/cutree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/decompose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/delete.response.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/dendrapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/deriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/deviance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/df.residual.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/diffinv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/dist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/dummy.coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ecdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/eff.aovlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/embed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/expand.model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/extractAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/factanal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/factor.scope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/family.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/fft.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/filter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/fisher.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/fitted.values.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/fivenum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/fligner.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/formula.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/friedman.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ftable.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/getInitial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/glm.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/glm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/heatmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/identify.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/influence.measures.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/integrate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/interaction.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/is.empty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/kernapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/kernel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/kmeans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/kruskal.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ks.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ksmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lag.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/line.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/listof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lm.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lmfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/loadings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/loess.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/logLik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/loglin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lowess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ls.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ls.print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/lsfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mad.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mahalanobis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/make.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/makepredictcall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mantelhaen.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mauchly.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mcnemar.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/median.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/medpolish.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/model.extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/model.tables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/monthplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/mood.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/na.action.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/na.contiguous.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/na.fail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nafns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/naprint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nextn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nlminb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nls.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/nobs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/numericDeriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/offset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/oneway.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/optim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/optimize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/order.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/p.adjust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/pairwise.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/pairwise.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/pairwise.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/pairwise.wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/plot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/poisson.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/poly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/power.anova.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/power.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/power.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/power.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/pp.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ppoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/prcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/predict.smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/preplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/print.power.htest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/print.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/printCoefmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/proj.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/prop.trend.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/qqnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/quade.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/quantile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/r2dtable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/rWishart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/read.ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/rect.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/relevel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/reorder.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/reorder.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/replications.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/reshape.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/runmed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/scatter.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/screeplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/sd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/se.contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/setNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/shapiro.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/sigma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/simulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/smoothEnds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/sortedXyData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/spec.ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/spec.pgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/spec.taper.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/spectrum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/splinefun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stat.anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stats-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stats-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stats-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/step.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/stlmethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/summary.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/supsmu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/symnum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/termplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/terms.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/terms.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/toeplitz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ts-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ts.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/ts.union.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/tsSmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/tsdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/tsp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/uniroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/update.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/var.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/varimax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/weighted.mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/weighted.residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/xtabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/zC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/coef-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/confint-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/logLik-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/mle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/plot-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/profile-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/profile.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/show-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/stats4-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/summary-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/summary.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/update-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/vcov-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/Surv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/agreg.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/anova.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/attrassign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/basehaz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/bladder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/cch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/cgd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/cgd0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/clogit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/cluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/coxph.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/coxph.detail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/coxph.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/coxph.wtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/dsurvreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/finegray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/flchain.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/frailty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/genfan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/heart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/is.ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/kidney.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/lines.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/logLik.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/logan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/lung.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/mgus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/mgus2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/model.frame.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/model.matrix.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/neardate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/nwtco.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/ovarian.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/pbc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/pbcseq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/plot.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/plot.cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/plot.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/predict.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/predict.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/print.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/print.summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/print.summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/print.summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/print.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/pspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/pyears.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/quantile.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/ratetableDate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/rats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/rats2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/residuals.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/residuals.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/retinopathy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/stanford2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/strata.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/summary.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survConcordance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survSplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survexp.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survexp.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survexp.us.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfit.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfit.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfit.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfit.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survfitcoxph.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survival-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survobrien.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survreg.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survreg.distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survreg.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/survregDtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/tcut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/tmerge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/tobin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/transplant.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/untangle.specials.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/uspop2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/survival/html/veteran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/TclInterface.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/TkCommands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/TkWidgetcmds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/TkWidgets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tclServiceMode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tcltk-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tcltk-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tkProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tkStartGUI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tk_choose.dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tk_choose.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tk_messageBox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tk_select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tcltk/html/tkpager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/HTMLheader.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/HTMLlinks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/QC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rcmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rd2HTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rd2txt_options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/RdTextFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rdindex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/Rdutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/SweaveTeXFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/add_datalist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/assertCondition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/bibstyle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/buildVignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/buildVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/charsets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkFF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkMD5sums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkPoFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkRdaFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkTnF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/checkVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/check_packages_in_dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/codoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/compactPDF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/delimMatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/dependsOnPkgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/encoded.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/fileutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/find_gs_cmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/getDepList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/getVignetteInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/installFoundDepends.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/loadRdMacros.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/makeLazyLoading.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/make_translations_pkg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/makevars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/md5sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/package.dependencies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/package_dependencies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/parseLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/parse_Rd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/print.via.format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/pskill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/psnice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/read.00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/showNonASCII.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/startDynamicHelp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/testInstalledPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/texi2dvi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/toHTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/toRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/toTitleCase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/tools-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/tools-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/tools-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/undoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/update_pkg_po.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/vignetteDepends.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/vignetteEngine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/writePACKAGES.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/tools/html/xgettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/BATCH.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/COMPILE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/INSTALL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/LINK.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/PkgUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Question.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/REMOVE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/RHOME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/RShowDoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/RSiteSearch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Rprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Rprofmem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Rscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Rtangle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/RweaveLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/SHLIB.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/Sweave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/SweaveSyntConv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/SweaveUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/URLencode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/View.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/adist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/alarm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/apropos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/aregexec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/aspell-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/aspell.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/available.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/bibentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/browseEnv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/browseURL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/browseVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/bug.report.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/capture.output.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/changedFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/chooseBioCmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/chooseCRANmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/citEntry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/citation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/cite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/close.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/combn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/compareVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/contrib.url.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/count.fields.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/create.post.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/dataentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/debugger.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/demo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/download.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/download.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/edit.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/example.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/file.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/filetest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/findLineNum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/fix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/flush.console.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/getAnywhere.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/getFromNamespace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/getParseData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/getS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/glob2rx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/globalVariables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/head.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/help.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/help.request.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/help.search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/help.start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/hsearch-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/install.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/installed.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/isS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/localeToCharset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/ls_str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/maintainer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/make.packages.html.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/make.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/memory.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/menu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/mirrorAdmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/modifyList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/news.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/nsl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/object.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/package.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/packageDescription.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/packageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/packageStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/page.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/person.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/process.events.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/prompt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/promptData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/promptPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/rcompgen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/read.DIF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/read.fortran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/read.fwf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/read.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/read.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/recover.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/relist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/remove.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/removeSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/roman.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/rtags.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/savehistory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/sessionInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/setRepositories.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/sourceutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/stack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/summaryRprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/tar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/toLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/txtProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/type.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/untar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/unzip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/update.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/url.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/utils-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/utils-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/utils-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/vignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.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-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/utils/html/zip.html
+ chmod +x /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/R/sh/echo.sh
+ chmod -x /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/CITATION /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/R-3.3.0/CAPABILITIES
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/include ']'
+ pushd /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R
+ ln -s ../../include/R include
~/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R ~/build/BUILD/R-3.3.0
~/build/BUILD/R-3.3.0
+ popd
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/texmf/tex/latex/R ']'
+ mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/texmf/tex/latex
~/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/texmf/tex/latex ~/build/BUILD/R-3.3.0
+ pushd /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/texmf/tex/latex
+ ln -s ../../../R/texmf/tex/latex R
~/build/BUILD/R-3.3.0
+ popd
+ /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-3.3.0
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/usr/lib/rpm/sepdebugcrcfix: Updated 35 CRC32s, 0 CRC32s did match.
cpio: /tmp/RtmpAXduNG/R.INSTALL1fa52739f75d/cluster/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpPJmXHr/R.INSTALL1afd5a504f0c/lattice/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpR5gvAu/R.INSTALL204254a6e66c/KernSmooth/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/AMD/Source: Cannot stat: No such file or directory
cpio: /tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/CHOLMOD/Lib: Cannot stat: No such file or directory
cpio: /tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/COLAMD/Source: Cannot stat: No such file or directory
cpio: /tmp/RtmpTI1cOu/R.INSTALL1b3015956199/Matrix/src/SuiteSparse_config: Cannot stat: No such file or directory
cpio: /tmp/RtmpUCf6aG/R.INSTALL1e3220ae4f24/nlme/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpXCqVNu/R.INSTALL1ace394755e4/MASS/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpZbQ7a6/R.INSTALL21016ef39a20/class/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpazimVu/R.INSTALL1ea31fdb2398/survival/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpnVX80A/R.INSTALL2089426aefa5/rpart/src: Cannot stat: No such file or directory
cpio: /tmp/Rtmpno8E2U/R.INSTALL211b60e350de/nnet/src: Cannot stat: No such file or directory
cpio: /tmp/Rtmpom9YA1/R.INSTALL1ffd7ceeb4eb/foreign/src: Cannot stat: No such file or directory
cpio: /tmp/RtmpuxstG4/R.INSTALL21416c3402d2/spatial/src: Cannot stat: No such file or directory
32537 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.WSXXG7
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.3.0
+ ulimit -s 16384
+ make check
make[1]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
  comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
  comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... OK
Testing examples for package 'datasets'
  comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
  comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
  comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
  comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests/Examples'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running strict specific tests
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running code in 'eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
  comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
running sloppy specific tests
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running code in 'complex.R' ... OK
  comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'print-tests.R' ... OK
  comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
  comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
  comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
  comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running regression tests ...
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running code in 'reg-tests-3.R' ... OK
  comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ... OK
  comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK
running tests of plotting Latin-1
  expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running tests of Internet functions
  expect some differences
make[3]: Entering directory `/builddir/build/BUILD/R-3.3.0/tests'
running code in 'internet.R' ... OK
  comparing 'internet.Rout' to './internet.Rout.save' ...11c11
< [1] 8624
---
> [1] 8269
 OK
make[3]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/tests'
+ exit 0
Processing files: R-3.3.0-3.el7.armv7hl
Provides: R = 3.3.0-3.el7 R(armv7hl-32) = 3.3.0-3.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-core-3.3.0-3.el7.armv7hl
Provides: R-KernSmooth = 2.23.15 R-MASS = 7.3.45 R-Matrix = 1.2.6 R-base = 3.3.0 R-boot = 1.3.18 R-class = 7.3.14 R-cluster = 2.0.4 R-codetools = 0.2.14 R-core = 3.3.0-3.el7 R-core(armv7hl-32) = 3.3.0-3.el7 R-datasets = 3.3.0 R-foreign = 0.8.66 R-grDevices = 3.3.0 R-graphics = 3.3.0 R-grid = 3.3.0 R-lattice = 0.20.33 R-methods = 3.3.0 R-mgcv = 1.8.12 R-nlme = 3.1.127 R-nnet = 7.3.12 R-parallel = 3.3.0 R-rpart = 4.1.10 R-spatial = 7.3.11 R-splines = 3.3.0 R-stats = 3.3.0 R-stats4 = 3.3.0 R-survival = 2.39.2 R-tcltk = 3.3.0 R-tools = 3.3.0 R-utils = 3.3.0 config(R-core) = 3.3.0-3.el7 libR.so libRblas.so libRlapack.so
Requires(interp): /bin/sh /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(preun): /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_3.3.1) 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 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-3.3.0-3.el7.armv7hl
Provides: R-Matrix-devel = 1.2.6 R-core-devel = 3.3.0-3.el7 R-core-devel(armv7hl-32) = 3.3.0-3.el7 pkgconfig(libR) = 3.3.0
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-3.3.0-3.el7.armv7hl
Provides: R-devel = 3.3.0-3.el7 R-devel(armv7hl-32) = 3.3.0-3.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-java-3.3.0-3.el7.armv7hl
Provides: R-java = 3.3.0-3.el7 R-java(armv7hl-32) = 3.3.0-3.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 = 3.3.0-3.el7 /bin/sh
Processing files: R-java-devel-3.3.0-3.el7.armv7hl
Provides: R-java-devel = 3.3.0-3.el7 R-java-devel(armv7hl-32) = 3.3.0-3.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 = 3.3.0-3.el7 java-devel /bin/sh
Processing files: libRmath-3.3.0-3.el7.armv7hl
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.smtbL9
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.3.0
+ DOCDIR=/builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/libRmath-3.3.0
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/libRmath-3.3.0
+ cp -pr doc/COPYING /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/share/doc/libRmath-3.3.0
+ exit 0
Provides: libRmath = 3.3.0-3.el7 libRmath(armv7hl-32) = 3.3.0-3.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-3.3.0-3.el7.armv7hl
Provides: libRmath-devel = 3.3.0-3.el7 libRmath-devel(armv7hl-32) = 3.3.0-3.el7 pkgconfig(libRmath) = 3.3.0
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-3.3.0-3.el7.armv7hl
Provides: libRmath-static = 3.3.0-3.el7 libRmath-static(armv7hl-32) = 3.3.0-3.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-debuginfo-3.3.0-3.el7.armv7hl
Provides: R-debuginfo = 3.3.0-3.el7 R-debuginfo(armv7hl-32) = 3.3.0-3.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-3.3.0-3.el7.arm
Wrote: /builddir/build/RPMS/R-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-core-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-core-devel-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-devel-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-java-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-java-devel-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-devel-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/libRmath-static-3.3.0-3.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/R-debuginfo-3.3.0-3.el7.armv7hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Tbxcy9
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.3.0
+ rm -rf /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm
+ exit 0
Child return code was: 0