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;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=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;\x07"', '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;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0private_network=Truelogger=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;\x07"', '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) ⅈ ^ 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 ' may be used uninitialized in this function [-Wmaybe-uninitialized] A( K+NB, NB ) = EI ^ cmplx.f:24668:0: warning: 'REALPART_EXPR ' 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 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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 -- 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`/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 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Rdutils html SweaveTeXFilter html add_datalist html assertCondition html bibstyle html buildVignette html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html Rd warning: /builddir/build/BUILD/R-3.3.0/src/library/tools/man/check_packages_in_dir.Rd:113: missing file link 'parLapply' codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html 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 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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 grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobName html grobWidth html grobX html legendGrob html makeContent html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html valid.just html validDetails html viewport html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory `/builddir/build/BUILD/R-3.3.0/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 Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done begin installing recommended package lattice * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** 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 cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done begin installing recommended package Matrix * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** 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 ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls-internal html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html varExp html varFixed html varFunc html varIdent html varPower html varWeights html varWeights.glsStruct html varWeights.lmeStruct html ** building package indices ** testing if installed package can be loaded * DONE (nlme) Making 'packages.html' ... done begin installing recommended package survival * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** 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 pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done begin installing recommended package mgcv * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** 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 Tweedie html 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' bam.update html bandchol html bug.reports.mgcv html cSplineDes html choose.k html columb html concurvity html coxph html exclude.too.far html extract.lme.cov html family.mgcv html fix.family.link html fixDependence html formXtViX html formula.gam html fs.test html full.score html gam html gam.check html gam.control html gam.convergence html gam.fit html gam.fit3 html gam.models html gam.outer html gam.scale html gam.selection html gam.side html gam.vcomp html gam2objective html gamObject html gamSim html gamm html gaulss html get.var html in.out html inSide html influence.gam html initial.sp html interpret.gam html jagam html ldTweedie html linear.functional.terms html logLik.gam html ls.size html magic html magic.post.proc html mgcv-FAQ html mgcv-package html mgcv-parallel html Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/mgcv-parallel.Rd:11: missing file link 'parallel' missing.data html model.matrix.gam html mono.con html mroot html multinom html mvn html negbin html new.name html notExp html notExp2 html null.space.dimension html ocat html pcls html pdIdnot html pdTens html pen.edf html place.knots html plot.gam html polys.plot html predict.bam html Rd warning: /tmp/RtmpOanF8b/R.INSTALL21614c1fb661/mgcv/man/predict.bam.Rd:76: missing file link 'parLapply' predict.gam html print.gam html qq.gam html rTweedie html random.effects html residuals.gam html rig html rmvn html s html scat html sdiag html single.index html slanczos html smooth.construct html smooth.construct.ad.smooth.spec html smooth.construct.bs.smooth.spec html smooth.construct.cr.smooth.spec html smooth.construct.ds.smooth.spec html smooth.construct.fs.smooth.spec html smooth.construct.gp.smooth.spec html smooth.construct.mrf.smooth.spec html smooth.construct.ps.smooth.spec html smooth.construct.re.smooth.spec html smooth.construct.so.smooth.spec html smooth.construct.sos.smooth.spec html smooth.construct.t2.smooth.spec html smooth.construct.tensor.smooth.spec html smooth.construct.tp.smooth.spec html smooth.terms html 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 ^ 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 make[1]: Leaving directory `/builddir/build/BUILD/R-3.3.0/src/nmath/standalone' + make pdf 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' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\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] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\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] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \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, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 338--341 [][][]\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] Underfull \hbox (badness 2359) in paragraph at lines 381--384 []\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] Underfull \hbox (badness 1072) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 848--848 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1135--1138 []\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] Underfull \hbox (badness 5862) in paragraph at lines 1369--1375 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1641--1647 []\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 Underfull \hbox (badness 3128) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 6094) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 10000) in paragraph at lines 1641--1647 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1651--1654 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 2865) in paragraph at lines 1753--1757 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1757--1759 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1894--1894 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1929--1931 []\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()) Underfull \hbox (badness 10000) in paragraph at lines 1932--1934 []\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 Underfull \hbox (badness 2012) in paragraph at lines 4030--4034 \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- Underfull \hbox (badness 2573) in paragraph at lines 4370--4373 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8475--8479 \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 , 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] Overfull \hbox (63.78036pt too wide) in paragraph at lines 13968--13968 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15760--15760 []\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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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] 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] 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] 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] 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] 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] Underfull \hbox (badness 2846) in paragraph at lines 41696--41700 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 41736--41736 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 41757--41761 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\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] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \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] Overfull \vbox (13.87083pt too high) has occurred while \output is active [658] Underfull \vbox (badness 1789) has occurred while \output is active [659] [660] Overfull \vbox (12.25539pt too high) has occurred while \output is active [661] [662] Overfull \vbox (17.12102pt too high) has occurred while \output is active [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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3696--3699 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [673] Overfull \vbox (10.49593pt too high) has occurred while \output is active [674] Underfull \hbox (badness 1173) in paragraph at lines 3830--3834 \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 . Overfull \vbox (27.49593pt too high) has occurred while \output is active [675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [686] [687] [688]) (./grDevices-pkg.tex Chapter 4. [689] [690] [691] [692] [693] [694] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\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] Underfull \hbox (badness 1248) in paragraph at lines 1347--1353 \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] Underfull \hbox (badness 10000) in paragraph at lines 1731--1737 [][][]\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [822] [823] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989 []\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] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [834] [835] Underfull \hbox (badness 5878) in paragraph at lines 2767--2771 \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 Underfull \hbox (badness 10000) in paragraph at lines 2792--2795 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2870--2873 [][][]\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] Underfull \hbox (badness 1755) in paragraph at lines 3130--3134 []\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] Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\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)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3407--3407 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [845] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3411--3411 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [846] [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [848] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3625--3625 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3677--3677 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3697--3697 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [850] Underfull \hbox (badness 10000) in paragraph at lines 3760--3764 [][][]\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] Underfull \hbox (badness 1286) in paragraph at lines 4383--4386 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4481--4481 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4485--4485 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [862] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4529--4529 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [863] Underfull \hbox (badness 1264) in paragraph at lines 4603--4616 \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] Underfull \hbox (badness 7925) in paragraph at lines 4740--4746 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [867 ] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 Underfull \vbox (badness 10000) has occurred while \output is active [868] [869 ] [870] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5178--5178 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [872] Underfull \hbox (badness 3954) in paragraph at lines 5280--5283 []\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] Underfull \hbox (badness 10000) in paragraph at lines 5336--5340 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5544--5544 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5545--5545 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5596--5600 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5596--5600 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5870--5870 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col. axis = "red")[] [882] [883] [884] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6022--6022 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6028--6028 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [885] [886] [887] [888] [889] [890] Underfull \hbox (badness 10000) in paragraph at lines 6455--6457 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [891] [892] Underfull \hbox (badness 1028) in paragraph at lines 6549--6551 []\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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [893 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [894] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6717--6717 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] Underfull \hbox (badness 10000) in paragraph at lines 6839--6841 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6866--6866 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [897] Underfull \hbox (badness 2600) in paragraph at lines 6932--6934 []\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] Underfull \hbox (badness 1881) in paragraph at lines 7121--7126 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7164--7164 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7551--7551 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7555--7555 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7567--7567 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7908--7908 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7911--7911 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [914] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7915--7915 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [915] [916] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8086--8086 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [917] [918] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8191--8191 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8202--8207 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8306--8306 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8321--8321 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [921] [922] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8625--8625 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8687--8693 []\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 \relax l.8735 \HeaderA{units}{Graphical Units}{units} [927] Underfull \hbox (badness 1205) in paragraph at lines 8800--8802 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8919--8919 []\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, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [947] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\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] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [958] [959] [960] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [961] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\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] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\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")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [972] [973] [974] [975] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [982] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6538--6538 []\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 Underfull \hbox (badness 5817) in paragraph at lines 278--285 \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[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1865--1865 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2258--2258 [] \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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 2441--2441 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1068] [1069] [1070] Underfull \hbox (badness 3792) in paragraph at lines 2655--2658 []\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] Underfull \hbox (badness 1194) in paragraph at lines 2686--2690 []\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] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2742--2742 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1073] [1074] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1075] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3041--3041 [] \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T RUE))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3043--3043 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3675--3684 [] [1085] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3764--3764 [] \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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4445--4445 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4446--4446 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] Underfull \vbox (badness 10000) has occurred while \output is active [1105] 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 \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 \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 \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 \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 \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 \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] 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 \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] 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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1374] [1375] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11439--11439 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1376] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11506--11506 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11518--11518 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1377] Underfull \hbox (badness 1062) in paragraph at lines 11566--11571 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1378] [1379] Underfull \hbox (badness 3623) in paragraph at lines 11711--11713 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$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 [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] 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), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18322--18322 []\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=)\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 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 [1634] [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28303--28303 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28331--28331 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1636] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1637] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28436--28436 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28513--28513 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1639] Underfull \hbox (badness 5050) in paragraph at lines 28549--28554 []\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] Underfull \hbox (badness 2205) in paragraph at lines 28602--28607 []\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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29198--29198 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1650] [1651] [1652] [1653] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\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 Underfull \hbox (badness 1596) in paragraph at lines 29483--29487 \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,[] 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] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29621--29621 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29630--29630 []\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] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30749--30749 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, Overfull \hbox (0.78088pt too wide) in paragraph at lines 30750--30750 [] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F ALSE)[] Underfull \hbox (badness 6775) in paragraph at lines 30788--30793 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30854--30854 [] \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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1680] [1681] [1682]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1683] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1691] [1692] [1693] Underfull \vbox (badness 10000) has occurred while \output is active [1694] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1490) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1706]) (./tools-pkg.tex Chapter 13. [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1708] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1709] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1710] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1711] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1712] [1713] [1714] Underfull \hbox (badness 10000) in paragraph at lines 540--541 [][][]$\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] Overfull \hbox (31.3804pt too wide) in paragraph at lines 950--950 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1722] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\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] Underfull \hbox (badness 5431) in paragraph at lines 1123--1126 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1154--1156 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1193--1196 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1327--1330 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1508--1508 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1511--1511 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] [1730] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1518--1523 \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 \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1734] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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] Underfull \hbox (badness 2644) in paragraph at lines 2139--2145 []\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] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2173--2173 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2174--2174 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2201--2208 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2201--2208 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2201--2208 \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] Underfull \hbox (badness 1342) in paragraph at lines 2251--2257 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2363--2363 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2376--2382 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 2411--2411 [] \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"),[] Underfull \hbox (badness 2486) in paragraph at lines 2564--2572 []\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] Underfull \hbox (badness 1072) in paragraph at lines 2942--2944 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3274--3274 [] \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3618--3618 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3621--3621 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3655--3661 []\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] Underfull \hbox (badness 7832) in paragraph at lines 3777--3780 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4002--4002 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4029--4034 []\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 Underfull \hbox (badness 2941) in paragraph at lines 4037--4043 \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] Underfull \hbox (badness 3758) in paragraph at lines 4117--4122 []\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- Underfull \hbox (badness 2865) in paragraph at lines 4117--4122 \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 4260--4272 \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] Underfull \hbox (badness 3623) in paragraph at lines 4321--4324 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 506--506 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 507--507 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 508--508 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 509--509 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 961--964 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1946--1946 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2066--2066 [] \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 \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 \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] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\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 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, Underfull \hbox (badness 6428) in paragraph at lines 10143--10152 \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 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, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2049] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\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] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\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] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\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] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\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 \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 \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2067] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \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"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2080] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2082] [2083] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \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 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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\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 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 Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2133] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [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] Underfull \hbox (badness 5119) in paragraph at lines 507--511 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 511--515 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 907--907 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2142] Underfull \hbox (badness 10000) in paragraph at lines 982--984 []\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 Underfull \hbox (badness 1092) in paragraph at lines 1005--1010 \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] Underfull \hbox (badness 10000) in paragraph at lines 1028--1035 []\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 \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 \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")}:] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1226--1226 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1320--1320 []\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 Underfull \hbox (badness 1609) in paragraph at lines 1395--1399 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1422--1422 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1436--1436 []\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() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1444--1444 []\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] Underfull \hbox (badness 1221) in paragraph at lines 1542--1548 \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 \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 \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 \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 \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 \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 Underfull \hbox (badness 1728) in paragraph at lines 1670--1674 \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] Underfull \hbox (badness 10000) in paragraph at lines 1761--1765 []\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] 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] 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 \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 \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 \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 \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 \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 \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 \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 \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),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9629--9629 []\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 \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"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9793--9793 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2251] Underfull \hbox (badness 6047) in paragraph at lines 9828--9840 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9845--9848 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9850--9851 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9854--9861 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9854--9861 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9867--9877 []\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- Underfull \hbox (badness 1194) in paragraph at lines 9901--9903 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2252] Underfull \hbox (badness 10000) in paragraph at lines 9915--9918 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 9924--9925 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 9930--9932 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 9934--9935 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 9942--9945 [][][]\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!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9964--9964 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 9985--9988 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10013--10015 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10021--10024 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10021--10024 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10032--10036 \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] Underfull \hbox (badness 6592) in paragraph at lines 10043--10045 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10120--10120 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10121--10121 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10122--10122 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2256] [2257] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10306--10306 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10307--10307 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2258] Underfull \hbox (badness 4621) in paragraph at lines 10347--10351 []\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] Underfull \hbox (badness 10000) in paragraph at lines 10423--10426 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 10435--10435 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10440--10440 []\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 \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, )\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] 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 Underfull \hbox (badness 10000) in paragraph at lines 2099--2102 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 Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [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 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 Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [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 \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],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400 [] \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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668 [] \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 153--153 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 154--154 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\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] 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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 1896--1896 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [2682] Underfull \vbox (badness 10000) has occurred while \output is active [2683] [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] Underfull \vbox (badness 10000) has occurred while \output is active [2697] 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] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2713] [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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5217--5217 []\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)[] Underfull \vbox (badness 10000) has occurred while \output is active [2729] [2730] [2731] [2732] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6314--6314 []\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)[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Underfull \vbox (badness 10000) has occurred while \output is active [2765] [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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7774--7774 [] \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[] Underfull \vbox (badness 10000) has occurred while \output is active [2783] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2810] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2828] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2834] 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))[] Underfull \vbox (badness 10000) has occurred while \output is active [2835] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2860] [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 \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 \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 \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 \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 \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 \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] 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 \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403 [] \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 \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3829--3829 []\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] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4270--4270 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3296] Underfull \hbox (badness 1540) in paragraph at lines 4325--4328 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4392--4392 []\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] 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] 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] Underfull \hbox (badness 10000) in paragraph at lines 5817--5826 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3318] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5927--5927 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6538--6538 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6812--6812 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3331] [3332] [3333] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7076--7076 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3334] Underfull \hbox (badness 1354) in paragraph at lines 7117--7121 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3335] [3336] Underfull \hbox (badness 2035) in paragraph at lines 7293--7300 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7293--7300 \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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7369--7369 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3338] [3339] [3340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7527--7527 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7659--7659 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7662--7662 [] \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7938--7938 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7939--7939 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7945--7945 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7947--7947 []\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. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\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] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\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] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \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, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 338--341 [][][]\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] Underfull \hbox (badness 2359) in paragraph at lines 381--384 []\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] Underfull \hbox (badness 1072) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 848--848 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1135--1138 []\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] Underfull \hbox (badness 5862) in paragraph at lines 1369--1375 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1641--1647 []\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 Underfull \hbox (badness 3128) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 6094) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 10000) in paragraph at lines 1641--1647 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1651--1654 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 2865) in paragraph at lines 1753--1757 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1757--1759 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1894--1894 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1929--1931 []\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()) Underfull \hbox (badness 10000) in paragraph at lines 1932--1934 []\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 Underfull \hbox (badness 2012) in paragraph at lines 4030--4034 \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- Underfull \hbox (badness 2573) in paragraph at lines 4370--4373 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8475--8479 \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 , 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] Overfull \hbox (63.78036pt too wide) in paragraph at lines 13968--13968 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15760--15760 []\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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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] 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] 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] 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] 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] 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] Underfull \hbox (badness 2846) in paragraph at lines 41696--41700 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 41736--41736 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 41757--41761 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\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] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \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] Overfull \vbox (13.87083pt too high) has occurred while \output is active [658] Underfull \vbox (badness 1789) has occurred while \output is active [659] [660] Overfull \vbox (12.25539pt too high) has occurred while \output is active [661] [662] Overfull \vbox (17.12102pt too high) has occurred while \output is active [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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3696--3699 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [673] Overfull \vbox (10.49593pt too high) has occurred while \output is active [674] Underfull \hbox (badness 1173) in paragraph at lines 3830--3834 \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 . Overfull \vbox (27.49593pt too high) has occurred while \output is active [675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [686] [687] [688]) (./grDevices-pkg.tex Chapter 4. [689] [690] [691] [692] [693] [694] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\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] Underfull \hbox (badness 1248) in paragraph at lines 1347--1353 \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] Underfull \hbox (badness 10000) in paragraph at lines 1731--1737 [][][]\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [822] [823] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989 []\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] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [834] [835] Underfull \hbox (badness 5878) in paragraph at lines 2767--2771 \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 Underfull \hbox (badness 10000) in paragraph at lines 2792--2795 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2870--2873 [][][]\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] Underfull \hbox (badness 1755) in paragraph at lines 3130--3134 []\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] Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\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)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3407--3407 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [845] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3411--3411 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [846] [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [848] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3625--3625 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3677--3677 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3697--3697 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [850] Underfull \hbox (badness 10000) in paragraph at lines 3760--3764 [][][]\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] Underfull \hbox (badness 1286) in paragraph at lines 4383--4386 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4481--4481 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4485--4485 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [862] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4529--4529 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [863] Underfull \hbox (badness 1264) in paragraph at lines 4603--4616 \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] Underfull \hbox (badness 7925) in paragraph at lines 4740--4746 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [867 ] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 Underfull \vbox (badness 10000) has occurred while \output is active [868] [869 ] [870] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5178--5178 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [872] Underfull \hbox (badness 3954) in paragraph at lines 5280--5283 []\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] Underfull \hbox (badness 10000) in paragraph at lines 5336--5340 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5544--5544 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5545--5545 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5596--5600 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5596--5600 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5870--5870 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col. axis = "red")[] [882] [883] [884] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6022--6022 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6028--6028 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [885] [886] [887] [888] [889] [890] Underfull \hbox (badness 10000) in paragraph at lines 6455--6457 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [891] [892] Underfull \hbox (badness 1028) in paragraph at lines 6549--6551 []\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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [893 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [894] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6717--6717 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] Underfull \hbox (badness 10000) in paragraph at lines 6839--6841 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6866--6866 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [897] Underfull \hbox (badness 2600) in paragraph at lines 6932--6934 []\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] Underfull \hbox (badness 1881) in paragraph at lines 7121--7126 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7164--7164 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7551--7551 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7555--7555 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7567--7567 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7908--7908 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7911--7911 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [914] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7915--7915 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [915] [916] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8086--8086 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [917] [918] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8191--8191 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8202--8207 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8306--8306 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8321--8321 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [921] [922] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8625--8625 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8687--8693 []\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 \relax l.8735 \HeaderA{units}{Graphical Units}{units} [927] Underfull \hbox (badness 1205) in paragraph at lines 8800--8802 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8919--8919 []\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, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [947] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\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] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [958] [959] [960] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [961] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\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] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\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")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [972] [973] [974] [975] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [982] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6538--6538 []\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 Underfull \hbox (badness 5817) in paragraph at lines 278--285 \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[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1865--1865 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2258--2258 [] \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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 2441--2441 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1068] [1069] [1070] Underfull \hbox (badness 3792) in paragraph at lines 2655--2658 []\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] Underfull \hbox (badness 1194) in paragraph at lines 2686--2690 []\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] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2742--2742 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1073] [1074] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1075] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3041--3041 [] \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T RUE))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3043--3043 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3675--3684 [] [1085] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3764--3764 [] \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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4445--4445 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4446--4446 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] Underfull \vbox (badness 10000) has occurred while \output is active [1105] 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 \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 \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 \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 \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 \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 \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] 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 \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] 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 \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 [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] 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), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18322--18322 []\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=)\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 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 [1634] [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28303--28303 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28331--28331 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1636] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1637] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28436--28436 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28513--28513 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1639] Underfull \hbox (badness 5050) in paragraph at lines 28549--28554 []\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] Underfull \hbox (badness 2205) in paragraph at lines 28602--28607 []\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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29198--29198 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1650] [1651] [1652] [1653] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\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 Underfull \hbox (badness 1596) in paragraph at lines 29483--29487 \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,[] 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] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29621--29621 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29630--29630 []\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] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30749--30749 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, Overfull \hbox (0.78088pt too wide) in paragraph at lines 30750--30750 [] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F ALSE)[] Underfull \hbox (badness 6775) in paragraph at lines 30788--30793 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30854--30854 [] \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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1680] [1681] [1682]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1683] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1691] [1692] [1693] Underfull \vbox (badness 10000) has occurred while \output is active [1694] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1490) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1706]) (./tools-pkg.tex Chapter 13. [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1708] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1709] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1710] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1711] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1712] [1713] [1714] Underfull \hbox (badness 10000) in paragraph at lines 540--541 [][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer / en / opentype / [1715] [1716] [1717] [1718] [1719] [1720] Overfull \hbox (0.78088pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1721] Overfull \hbox (31.3804pt too wide) in paragraph at lines 950--950 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1722] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\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] Underfull \hbox (badness 5431) in paragraph at lines 1123--1126 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1154--1156 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1193--1196 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1327--1330 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1508--1508 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1511--1511 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] [1730] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1518--1523 \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 \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1734] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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] Underfull \hbox (badness 2644) in paragraph at lines 2139--2145 []\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] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2173--2173 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2174--2174 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2201--2208 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2201--2208 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2201--2208 \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] Underfull \hbox (badness 1342) in paragraph at lines 2251--2257 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2363--2363 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2376--2382 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 2411--2411 [] \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"),[] Underfull \hbox (badness 2486) in paragraph at lines 2564--2572 []\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] Underfull \hbox (badness 1072) in paragraph at lines 2942--2944 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3274--3274 [] \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3618--3618 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3621--3621 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3655--3661 []\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] Underfull \hbox (badness 7832) in paragraph at lines 3777--3780 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4002--4002 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4029--4034 []\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 Underfull \hbox (badness 2941) in paragraph at lines 4037--4043 \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] Underfull \hbox (badness 3758) in paragraph at lines 4117--4122 []\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- Underfull \hbox (badness 2865) in paragraph at lines 4117--4122 \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 4260--4272 \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] Underfull \hbox (badness 3623) in paragraph at lines 4321--4324 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 506--506 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 507--507 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 508--508 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 509--509 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 961--964 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1946--1946 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2066--2066 [] \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 \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 \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] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\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 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$[][]\T1/ptm/m/n/10 . [1918] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9757--9757 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9761--9761 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1919] [1920] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9893--9893 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1921] [1922] [1923] Underfull \hbox (badness 8075) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via Underfull \hbox (badness 6725) in paragraph at lines 10143--10152 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10143--10152 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10143--10152 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10143--10152 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1924] [1925] Underfull \hbox (badness 3646) in paragraph at lines 10269--10271 [][][]$\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 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, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2049] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\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] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\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] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\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] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\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 \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 \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2067] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \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"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2080] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2082] [2083] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \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 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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\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 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 Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2133] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [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] Underfull \hbox (badness 5119) in paragraph at lines 507--511 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 511--515 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 907--907 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2142] Underfull \hbox (badness 10000) in paragraph at lines 982--984 []\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 Underfull \hbox (badness 1092) in paragraph at lines 1005--1010 \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] Underfull \hbox (badness 10000) in paragraph at lines 1028--1035 []\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 \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 \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")}:] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1226--1226 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1320--1320 []\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 Underfull \hbox (badness 1609) in paragraph at lines 1395--1399 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1422--1422 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1436--1436 []\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() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1444--1444 []\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] Underfull \hbox (badness 1221) in paragraph at lines 1542--1548 \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 \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 \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 \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 \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 \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 Underfull \hbox (badness 1728) in paragraph at lines 1670--1674 \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] Underfull \hbox (badness 10000) in paragraph at lines 1761--1765 []\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] 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] 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 \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 \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 \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 \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 \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 \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 \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 \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),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9629--9629 []\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 \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"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9793--9793 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2251] Underfull \hbox (badness 6047) in paragraph at lines 9828--9840 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9845--9848 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9850--9851 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9854--9861 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9854--9861 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9867--9877 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 9867--9877 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- Underfull \hbox (badness 1194) in paragraph at lines 9901--9903 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2252] Underfull \hbox (badness 10000) in paragraph at lines 9915--9918 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 9924--9925 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 9930--9932 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 9934--9935 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 9942--9945 [][][]\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!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9964--9964 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 9985--9988 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10013--10015 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10021--10024 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10021--10024 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10032--10036 \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] Underfull \hbox (badness 6592) in paragraph at lines 10043--10045 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10120--10120 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10121--10121 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10122--10122 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2256] [2257] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10306--10306 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10307--10307 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2258] Underfull \hbox (badness 4621) in paragraph at lines 10347--10351 []\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] Underfull \hbox (badness 10000) in paragraph at lines 10423--10426 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 10435--10435 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10440--10440 []\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 \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, )\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] 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 Underfull \hbox (badness 10000) in paragraph at lines 2099--2102 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 Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2482] [2483] Underfull \hbox (badness 3601) in paragraph at lines 234--242 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2484] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2485] [2486] [2487] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame)[] [2488] Underfull \hbox (badness 10000) in paragraph at lines 519--527 []\T1/ptm/m/n/10 URL [][]$\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 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 Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [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 \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")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668 [] \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 153--153 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 154--154 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\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] 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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 1896--1896 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [2682] Underfull \vbox (badness 10000) has occurred while \output is active [2683] [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] Underfull \vbox (badness 10000) has occurred while \output is active [2697] 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] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2713] [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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5217--5217 []\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$jags.in i,n.chains=1)[] Underfull \vbox (badness 10000) has occurred while \output is active [2729] [2730] [2731] [2732] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [2734] [2735] Overfull \hbox (52.98038pt too wide) in paragraph at lines 5637--5637 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5664--5664 [] \T1/pcr/m/n/10 .Machine$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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6314--6314 []\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)[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Underfull \vbox (badness 10000) has occurred while \output is active [2765] [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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7774--7774 [] \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[] Underfull \vbox (badness 10000) has occurred while \output is active [2783] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2810] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2828] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2834] 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))[] Underfull \vbox (badness 10000) has occurred while \output is active [2835] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2860] [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 \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 \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 \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 \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 \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 \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] 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 \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403 [] \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 \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3829--3829 []\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] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4270--4270 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3296] Underfull \hbox (badness 1540) in paragraph at lines 4325--4328 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4392--4392 []\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] 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] 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] Underfull \hbox (badness 10000) in paragraph at lines 5817--5826 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3318] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5927--5927 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6538--6538 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6812--6812 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3331] [3332] [3333] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7076--7076 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3334] Underfull \hbox (badness 1354) in paragraph at lines 7117--7121 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3335] [3336] Underfull \hbox (badness 2035) in paragraph at lines 7293--7300 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7293--7300 \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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7369--7369 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3338] [3339] [3340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7527--7527 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7659--7659 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7662--7662 [] \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7938--7938 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7939--7939 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7945--7945 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7947--7947 []\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] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2164--2166 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2166--2168 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2168--2170 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , [3373] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2170--2172 []| \T1/pcr/m/n/10 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paragraph at lines 2731--2733 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2733--2735 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2735--2737 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3379] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2865--2867 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] Overfull \hbox (62.8567pt too wide) in paragraph at lines 3810--3812 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3812--3814 []\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3814--3816 []\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method Overfull \hbox (20.8567pt too wide) 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cbind2,sparseMatrix,sparseMatrix-method [3405] Overfull \hbox (10.01662pt too wide) in paragraph at lines 6648--6650 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3406] [3407] Underfull \vbox (badness 1484) has occurred while \output is active [3408] Overfull \hbox (50.8567pt too wide) in paragraph at lines 7116--7118 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7118--7120 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7120--7122 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7126--7128 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7128--7130 []\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7132--7134 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at lines 7256--7258 []\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method Underfull \vbox (badness 3769) has occurred while \output is active [3410] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7262--7264 []\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7264--7266 []\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7270--7272 []\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7272--7274 []\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7278--7280 []\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7280--7282 []\T1/pcr/m/n/10 coerce,dsCMatrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7282--7284 []\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 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paragraph at lines 7304--7306 []\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7306--7308 []\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7308--7310 []\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7310--7312 []\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7312--7314 []\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7314--7316 []\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7318--7320 []\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7320--7322 []\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7322--7324 []\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7324--7326 []\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7326--7328 []\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7328--7330 []\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7332--7334 []\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7334--7336 []\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7336--7338 []\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7338--7340 []\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7340--7342 []\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7342--7344 []\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7346--7348 []\T1/pcr/m/n/10 coerce,dtCMatrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7348--7350 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7350--7352 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7352--7354 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7354--7356 []\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7356--7358 []\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7358--7360 []\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method Overfull 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[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7408--7410 []\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7410--7412 []\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7412--7414 []\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7414--7416 []\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7416--7418 []\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7418--7420 []\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7422--7424 []\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7426--7428 []\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7430--7432 []\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7432--7434 []\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7436--7438 []\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7438--7440 []\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7444--7446 []\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7446--7448 []\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7448--7450 []\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7450--7452 []\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7452--7454 []\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7454--7456 []\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7456--7458 []\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7458--7460 []\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7460--7462 []\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method Underfull \vbox (badness 3769) has occurred while \output is active [3412] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7462--7464 []\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7464--7466 []\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7466--7468 []\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7468--7470 []\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7470--7472 []\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7474--7476 []\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7476--7478 []\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7478--7480 []\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7480--7482 []\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7482--7484 []\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7484--7486 []\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7486--7488 []\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7490--7492 []\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7492--7494 []\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7494--7496 []\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7496--7498 []\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7498--7500 []\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7500--7502 []\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7504--7506 []\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7506--7508 []\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7518--7520 []\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7520--7522 []\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7522--7524 []\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7524--7526 []\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7526--7528 []\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7528--7530 []\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7532--7534 []\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7534--7536 []\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7536--7538 []\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7538--7540 []\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method Underfull \vbox (badness 6876) has occurred while \output is active [3413] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7540--7542 []\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7542--7544 []\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7544--7546 []\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7546--7548 []\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7548--7550 []\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7550--7552 []\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7554--7556 []\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7556--7558 []\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7558--7560 []\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7562--7564 []\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7564--7566 []\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7566--7568 []\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7570--7572 []\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7572--7574 []\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7574--7576 []\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7576--7578 []\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7578--7580 []\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 7580--7582 []\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7582--7584 []\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7584--7586 []\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7586--7588 []\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7588--7590 []\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7590--7592 []\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7592--7594 []\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7602--7604 []\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7604--7606 []\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7606--7608 []\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7616--7618 []\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7618--7620 []\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method Underfull \vbox (badness 5022) has occurred while \output is active [3414] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7648--7650 []\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7678--7680 []\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7704--7706 []\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7706--7708 []\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7708--7710 []\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7710--7712 []\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7712--7714 []\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active [3415] Overfull \hbox (14.8567pt too wide) in paragraph at lines 7714--7716 []\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7718--7720 []\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7720--7722 []\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7722--7724 []\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7726--7728 []\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7728--7730 []\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7730--7732 []\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7734--7736 []\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7736--7738 []\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7738--7740 []\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7740--7742 []\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7744--7746 []\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7746--7748 []\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7748--7750 []\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7750--7752 []\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7752--7754 []\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7754--7756 []\T1/pcr/m/n/10 coerce,ndenseMatrix,nsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7756--7758 []\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7758--7760 []\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7760--7762 []\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method Underfull \vbox (badness 2903) has occurred while \output is active Overfull \hbox (32.8567pt too wide) in paragraph at lines 7764--7766 []\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7766--7768 []\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7770--7772 []\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7774--7776 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7776--7778 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7778--7780 []\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7780--7782 []\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7782--7784 []\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7786--7788 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7788--7790 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7790--7792 []\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7792--7794 []\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7794--7796 []\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7796--7798 []\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7798--7800 []\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7800--7802 []\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active [3416] Overfull \hbox (32.8567pt too wide) in paragraph at lines 7804--7806 []\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7806--7808 []\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7808--7810 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7810--7812 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7816--7818 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7818--7820 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7820--7822 []\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7822--7824 []\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7824--7826 []\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7838--7840 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7840--7842 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7842--7844 []\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7846--7848 []\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7848--7850 []\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7852--7854 []\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7854--7856 []\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7856--7858 []\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7858--7860 []\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7880--7882 []\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method [3417] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7882--7884 []\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7884--7886 []\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7886--7888 []\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7888--7890 []\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7890--7892 []\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7892--7894 []\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7896--7898 []\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7898--7900 []\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7902--7904 []\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7904--7906 []\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7908--7910 []\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7910--7912 []\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7912--7914 []\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7914--7916 []\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7916--7918 []\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 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paragraph at lines 7936--7938 []\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7938--7940 []\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7940--7942 []\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7944--7946 []\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7952--7954 []\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7958--7960 []\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7962--7964 []\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active [3418] Overfull \hbox (20.8567pt too wide) in paragraph at lines 7966--7968 []\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7978--7980 []\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7980--7982 []\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7982--7984 []\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7984--7986 []\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7986--7988 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7988--7990 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7990--7992 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7992--7994 []\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7994--7996 []\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7996--7998 []\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7998--8000 []\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8000--8002 []\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8002--8004 []\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8004--8006 []\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8010--8012 []\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8012--8014 []\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8014--8016 []\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8016--8018 []\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8018--8020 []\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8020--8022 []\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8022--8024 []\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8024--8026 []\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8026--8028 []\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8028--8030 []\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8030--8032 []\T1/pcr/m/n/10 coerce,sparseVector,integer-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8032--8034 []\T1/pcr/m/n/10 coerce,sparseVector,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8034--8036 []\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8036--8038 []\T1/pcr/m/n/10 coerce,sparseVector,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8038--8040 []\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8040--8042 []\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8042--8044 []\T1/pcr/m/n/10 coerce,sparseVector,vector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8044--8046 []\T1/pcr/m/n/10 coerce,table,sparseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8046--8048 []\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8048--8050 []\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8050--8052 []\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8052--8054 []\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8054--8056 []\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8056--8058 []\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8058--8060 []\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8060--8062 []\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8062--8064 []\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8064--8066 []\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8066--8068 []\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method Underfull \vbox (badness 2903) has occurred while \output is active [3419] Overfull \hbox (56.8567pt too wide) in paragraph at lines 8068--8070 []\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8070--8072 []\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8072--8074 []\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8204--8206 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8210--8212 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Underfull \vbox (badness 1117) has occurred while \output is active [3420] Overfull \hbox (62.8567pt too wide) in paragraph at lines 8222--8224 []\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8224--8226 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8238--8240 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3421] [3422] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 8736--8738 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8738--8740 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 8740--8742 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8742--8744 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8744--8746 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8746--8748 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8748--8750 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8750--8752 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,ddenseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8752--8754 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 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(\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3439] Overfull \hbox (20.8567pt too wide) in paragraph at lines 12100--12102 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [3440] [3441] [3442] [3443] Overfull \hbox (8.8567pt too wide) in paragraph at lines 12819--12821 []\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12821--12823 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12829--12831 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method [3444] Overfull \hbox (2.8567pt too wide) in paragraph at lines 12990--12992 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12996--12998 []\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12998--13000 []\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method Overfull \hbox (8.8567pt 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paragraph at lines 13118--13120 []\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method Underfull \vbox (badness 2564) has occurred while \output is active Overfull \hbox (20.8567pt too wide) in paragraph at lines 13209--13211 []\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13213--13215 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13215--13217 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13217--13219 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method [3446] Overfull \hbox (20.8567pt too wide) in paragraph at lines 13219--13221 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13221--13223 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13223--13225 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13225--13227 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13227--13229 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13229--13231 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13233--13235 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13235--13237 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13237--13239 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13239--13241 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13241--13243 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3447] [3448] [3449] Overfull \hbox (50.8567pt too wide) in paragraph at lines 13965--13967 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13971--13973 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 13973--13975 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13975--13977 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13977--13979 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13979--13981 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Underfull \vbox (badness 1348) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 13985--13987 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13995--13997 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 13997--13999 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 13999--14001 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 14001--14003 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14003--14005 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14011--14013 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14021--14023 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 14023--14025 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Underfull \vbox (badness 3302) has occurred while \output is active [3450] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14031--14033 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14033--14035 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14035--14037 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14037--14039 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14039--14041 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3451] [3452] [3453] [3454] Overfull \hbox (52.01662pt too wide) in paragraph at lines 14973--14975 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3455] [3456] Overfull \hbox (8.8567pt too wide) in paragraph at lines 15491--15493 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 15510--15512 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15512--15514 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15518--15520 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Underfull \vbox (badness 1019) has occurred while \output is active [3457] Overfull \hbox (14.8567pt too wide) in paragraph at lines 15536--15538 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15542--15544 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15544--15546 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3458] Overfull \hbox (26.8567pt too wide) in paragraph at lines 15783--15785 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15789--15791 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15801--15803 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15803--15805 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 15805--15807 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15807--15809 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 15809--15811 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method Underfull \vbox (badness 6876) has occurred while \output is active [3459] Overfull \hbox (38.8567pt too wide) in paragraph at lines 15829--15831 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15831--15833 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15847--15849 []\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (38.8567pt too wide) in paragraph at lines 15867--15869 []\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15869--15871 []\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15887--15889 []\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15895--15897 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method [3460] Overfull \hbox (38.8567pt too wide) in paragraph at lines 15899--15901 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15901--15903 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15903--15905 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15921--15923 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15923--15925 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15925--15927 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15927--15929 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15931--15933 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15935--15937 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15939--15941 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3461] Overfull \hbox (46.01662pt too wide) in paragraph at lines 16125--16127 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3462] [3463] [3464] [3465] [3466] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17382--17384 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17385--17387 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17387--17389 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17389--17391 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17391--17393 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17393--17395 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 17395--17397 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3467] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17397--17399 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17399--17401 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17401--17403 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 17405--17407 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17407--17409 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17409--17411 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17411--17413 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17413--17415 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17415--17417 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Underfull \vbox (badness 2564) has occurred while \output is active [3468] [3469] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17752--17754 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17822--17824 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3470] [3471] [3472] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18274--18276 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18283--18285 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18285--18287 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18287--18289 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18289--18291 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18301--18303 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18311--18313 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 18326--18328 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18332--18334 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3473] [3474] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18638--18640 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18640--18642 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18642--18644 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18644--18646 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 18648--18650 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18650--18652 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18652--18654 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18654--18656 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 18656--18658 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18658--18660 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18660--18662 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18666--18668 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18670--18672 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18680--18682 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18684--18686 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18686--18688 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18688--18690 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 18690--18692 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18692--18694 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18694--18696 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 18696--18698 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18725--18727 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18727--18729 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18729--18731 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18731--18733 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method [3475] Overfull \hbox (2.8567pt too wide) in paragraph at lines 18735--18737 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18739--18741 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18743--18745 []\T1/pcr/m/n/10 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\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] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\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] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \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, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \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 Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 338--341 [][][]\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] Underfull \hbox (badness 2359) in paragraph at lines 381--384 []\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] Underfull \hbox (badness 1072) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 848--848 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1135--1138 []\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] Underfull \hbox (badness 5862) in paragraph at lines 1369--1375 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1641--1647 []\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 Underfull \hbox (badness 3128) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 6094) in paragraph at lines 1641--1647 \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 Underfull \hbox (badness 10000) in paragraph at lines 1641--1647 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1651--1654 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 2865) in paragraph at lines 1753--1757 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1757--1759 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1894--1894 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1929--1931 []\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()) Underfull \hbox (badness 10000) in paragraph at lines 1932--1934 []\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 Underfull \hbox (badness 2012) in paragraph at lines 4030--4034 \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- Underfull \hbox (badness 2573) in paragraph at lines 4370--4373 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8475--8479 \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 , 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] Overfull \hbox (63.78036pt too wide) in paragraph at lines 13968--13968 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15760--15760 []\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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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] 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] 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] 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] 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] 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] Underfull \hbox (badness 2846) in paragraph at lines 41696--41700 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 41736--41736 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 41757--41761 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\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] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \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] Overfull \vbox (13.87083pt too high) has occurred while \output is active [658] Underfull \vbox (badness 1789) has occurred while \output is active [659] [660] Overfull \vbox (12.25539pt too high) has occurred while \output is active [661] [662] Overfull \vbox (17.12102pt too high) has occurred while \output is active [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] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3696--3699 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [673] Overfull \vbox (10.49593pt too high) has occurred while \output is active [674] Underfull \hbox (badness 1173) in paragraph at lines 3830--3834 \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 . Overfull \vbox (27.49593pt too high) has occurred while \output is active [675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [686] [687] [688]) (./grDevices-pkg.tex Chapter 4. [689] [690] [691] [692] [693] [694] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\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] Underfull \hbox (badness 1248) in paragraph at lines 1347--1353 \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] Underfull \hbox (badness 10000) in paragraph at lines 1731--1737 [][][]\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [822] [823] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989 []\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] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [834] [835] Underfull \hbox (badness 5878) in paragraph at lines 2767--2771 \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 Underfull \hbox (badness 10000) in paragraph at lines 2792--2795 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2870--2873 [][][]\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] Underfull \hbox (badness 1755) in paragraph at lines 3130--3134 []\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] Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3205--3210 [][]\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)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3407--3407 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [845] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3411--3411 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [846] [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [848] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3625--3625 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3677--3677 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3697--3697 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [850] Underfull \hbox (badness 10000) in paragraph at lines 3760--3764 [][][]\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] Underfull \hbox (badness 1286) in paragraph at lines 4383--4386 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4481--4481 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4485--4485 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [862] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4529--4529 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [863] Underfull \hbox (badness 1264) in paragraph at lines 4603--4616 \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] Underfull \hbox (badness 7925) in paragraph at lines 4740--4746 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [867 ] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 Underfull \vbox (badness 10000) has occurred while \output is active [868] [869 ] [870] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5178--5178 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [872] Underfull \hbox (badness 3954) in paragraph at lines 5280--5283 []\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] Underfull \hbox (badness 10000) in paragraph at lines 5336--5340 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5544--5544 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5545--5545 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5596--5600 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5596--5600 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5870--5870 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col. axis = "red")[] [882] [883] [884] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6022--6022 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6028--6028 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [885] [886] [887] [888] [889] [890] Underfull \hbox (badness 10000) in paragraph at lines 6455--6457 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [891] [892] Underfull \hbox (badness 1028) in paragraph at lines 6549--6551 []\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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [893 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [894] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6717--6717 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] Underfull \hbox (badness 10000) in paragraph at lines 6839--6841 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6866--6866 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [897] Underfull \hbox (badness 2600) in paragraph at lines 6932--6934 []\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] Underfull \hbox (badness 1881) in paragraph at lines 7121--7126 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7164--7164 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7551--7551 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7555--7555 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7567--7567 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7908--7908 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7911--7911 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [914] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7915--7915 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [915] [916] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8086--8086 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [917] [918] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8191--8191 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8202--8207 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8306--8306 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8321--8321 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [921] [922] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8625--8625 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8687--8693 []\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 \relax l.8735 \HeaderA{units}{Graphical Units}{units} [927] Underfull \hbox (badness 1205) in paragraph at lines 8800--8802 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8919--8919 []\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, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [947] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\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] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [958] [959] [960] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [961] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\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] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\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")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [972] [973] [974] [975] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [982] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6538--6538 []\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 Underfull \hbox (badness 5817) in paragraph at lines 278--285 \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[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1865--1865 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2258--2258 [] \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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 2441--2441 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1068] [1069] [1070] Underfull \hbox (badness 3792) in paragraph at lines 2655--2658 []\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] Underfull \hbox (badness 1194) in paragraph at lines 2686--2690 []\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] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2742--2742 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1073] [1074] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1075] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3041--3041 [] \T1/pcr/m/n/10 resolve.msg = getOption("getClass.msg", default=T RUE))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3043--3043 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3675--3684 [] [1085] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3764--3764 [] \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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4445--4445 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4446--4446 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] Underfull \vbox (badness 10000) has occurred while \output is active [1105] 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 \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 \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 \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 \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 \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 \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] 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 \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] 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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1374] [1375] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11439--11439 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1376] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11506--11506 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11518--11518 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1377] Underfull \hbox (badness 1062) in paragraph at lines 11566--11571 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1378] [1379] Underfull \hbox (badness 3623) in paragraph at lines 11711--11713 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$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 [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] 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), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18322--18322 []\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=)\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 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 [1634] [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28303--28303 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28331--28331 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1636] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1637] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28436--28436 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28513--28513 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1639] Underfull \hbox (badness 5050) in paragraph at lines 28549--28554 []\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] Underfull \hbox (badness 2205) in paragraph at lines 28602--28607 []\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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29198--29198 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1650] [1651] [1652] [1653] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\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 Underfull \hbox (badness 1596) in paragraph at lines 29483--29487 \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,[] 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] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29621--29621 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29630--29630 []\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] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30749--30749 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, Overfull \hbox (0.78088pt too wide) in paragraph at lines 30750--30750 [] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F ALSE)[] Underfull \hbox (badness 6775) in paragraph at lines 30788--30793 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30854--30854 [] \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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1680] [1681] [1682]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1683] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1691] [1692] [1693] Underfull \vbox (badness 10000) has occurred while \output is active [1694] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1490) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1706]) (./tools-pkg.tex Chapter 13. [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1708] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1709] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1710] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1711] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1712] [1713] [1714] Underfull \hbox (badness 10000) in paragraph at lines 540--541 [][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer / en / opentype / [1715] [1716] [1717] [1718] [1719] [1720] Overfull \hbox (0.78088pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1721] Overfull \hbox (31.3804pt too wide) in paragraph at lines 950--950 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1722] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\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] Underfull \hbox (badness 5431) in paragraph at lines 1123--1126 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1154--1156 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1185--1188 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1193--1196 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1327--1330 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1508--1508 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1511--1511 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] [1730] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1518--1523 \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 \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1734] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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 Underfull \hbox (badness 10000) in paragraph at lines 1836--1841 \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] Underfull \hbox (badness 2644) in paragraph at lines 2139--2145 []\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] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2173--2173 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2174--2174 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2201--2208 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2201--2208 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2201--2208 \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] Underfull \hbox (badness 1342) in paragraph at lines 2251--2257 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2363--2363 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2376--2382 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 2411--2411 [] \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"),[] Underfull \hbox (badness 2486) in paragraph at lines 2564--2572 []\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] Underfull \hbox (badness 1072) in paragraph at lines 2942--2944 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3274--3274 [] \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3618--3618 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3621--3621 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3655--3661 []\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] Underfull \hbox (badness 7832) in paragraph at lines 3777--3780 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4002--4002 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4029--4034 []\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 Underfull \hbox (badness 2941) in paragraph at lines 4037--4043 \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] Underfull \hbox (badness 3758) in paragraph at lines 4117--4122 []\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- Underfull \hbox (badness 2865) in paragraph at lines 4117--4122 \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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 4260--4272 \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] Underfull \hbox (badness 3623) in paragraph at lines 4321--4324 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 506--506 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 507--507 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 508--508 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 509--509 [] \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] Underfull \hbox (badness 10000) in paragraph at lines 961--964 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1946--1946 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2066--2066 [] \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 \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 \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] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\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 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$[][]\T1/ptm/m/n/10 . [1918] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9757--9757 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9761--9761 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1919] [1920] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9893--9893 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1921] [1922] [1923] Underfull \hbox (badness 8075) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via Underfull \hbox (badness 6725) in paragraph at lines 10143--10152 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10143--10152 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10143--10152 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10143--10152 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1924] [1925] Underfull \hbox (badness 3646) in paragraph at lines 10269--10271 [][][]$\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 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, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\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] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2049] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\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] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\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] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\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] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\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 \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 \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2067] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \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"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2080] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2082] [2083] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \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 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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\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 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 Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2133] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [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] Underfull \hbox (badness 5119) in paragraph at lines 507--511 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 511--515 []\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] Overfull \hbox (72.78088pt too wide) in paragraph at lines 907--907 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2142] Underfull \hbox (badness 10000) in paragraph at lines 982--984 []\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 Underfull \hbox (badness 1092) in paragraph at lines 1005--1010 \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] Underfull \hbox (badness 10000) in paragraph at lines 1028--1035 []\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 \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 \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")}:] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1226--1226 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1320--1320 []\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 Underfull \hbox (badness 1609) in paragraph at lines 1395--1399 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1422--1422 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1436--1436 []\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() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1444--1444 []\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] Underfull \hbox (badness 1221) in paragraph at lines 1542--1548 \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 \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 \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 \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 \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 \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 Underfull \hbox (badness 1728) in paragraph at lines 1670--1674 \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] Underfull \hbox (badness 10000) in paragraph at lines 1761--1765 []\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] 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] 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 \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 \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 \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 \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 \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 \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 \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 \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),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9629--9629 []\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 \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"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9793--9793 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2251] Underfull \hbox (badness 6047) in paragraph at lines 9828--9840 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9845--9848 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9850--9851 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9854--9861 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9854--9861 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9867--9877 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 9867--9877 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- Underfull \hbox (badness 1194) in paragraph at lines 9901--9903 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2252] Underfull \hbox (badness 10000) in paragraph at lines 9915--9918 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 9924--9925 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 9930--9932 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 9934--9935 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 9942--9945 [][][]\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!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9964--9964 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 9985--9988 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10013--10015 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10021--10024 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10021--10024 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10032--10036 \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] Underfull \hbox (badness 6592) in paragraph at lines 10043--10045 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10120--10120 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10121--10121 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10122--10122 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2256] [2257] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10306--10306 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10307--10307 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2258] Underfull \hbox (badness 4621) in paragraph at lines 10347--10351 []\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] Underfull \hbox (badness 10000) in paragraph at lines 10423--10426 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 10435--10435 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10440--10440 []\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 \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, )\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] 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 Underfull \hbox (badness 10000) in paragraph at lines 2099--2102 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 Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2482] [2483] Underfull \hbox (badness 3601) in paragraph at lines 234--242 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2484] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2485] [2486] [2487] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame)[] [2488] Underfull \hbox (badness 10000) in paragraph at lines 519--527 []\T1/ptm/m/n/10 URL [][]$\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 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 Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [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 \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")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$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] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668 [] \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 153--153 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 154--154 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\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] 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 Overfull \hbox (6.78088pt too wide) in paragraph at lines 1896--1896 []\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] Underfull \vbox (badness 10000) has occurred while \output is active [2682] Underfull \vbox (badness 10000) has occurred while \output is active [2683] [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] Underfull \vbox (badness 10000) has occurred while \output is active [2697] 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] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2713] [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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5217--5217 []\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$jags.in i,n.chains=1)[] Underfull \vbox (badness 10000) has occurred while \output is active [2729] [2730] [2731] [2732] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [2734] [2735] Overfull \hbox (52.98038pt too wide) in paragraph at lines 5637--5637 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5664--5664 [] \T1/pcr/m/n/10 .Machine$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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6314--6314 []\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)[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Underfull \vbox (badness 10000) has occurred while \output is active [2765] [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] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7774--7774 [] \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[] Underfull \vbox (badness 10000) has occurred while \output is active [2783] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2810] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2828] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2834] 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))[] Underfull \vbox (badness 10000) has occurred while \output is active [2835] 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] Underfull \vbox (badness 10000) has occurred while \output is active [2860] [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 \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 \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 \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 \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 \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 \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] 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 \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 \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] Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403 [] \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 \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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3829--3829 []\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] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4270--4270 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3296] Underfull \hbox (badness 1540) in paragraph at lines 4325--4328 []\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] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4392--4392 []\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] 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] 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] Underfull \hbox (badness 10000) in paragraph at lines 5817--5826 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3318] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5927--5927 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6538--6538 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6812--6812 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3331] [3332] [3333] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7076--7076 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3334] Underfull \hbox (badness 1354) in paragraph at lines 7117--7121 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3335] [3336] Underfull \hbox (badness 2035) in paragraph at lines 7293--7300 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7293--7300 \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] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7369--7369 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3338] [3339] [3340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7527--7527 [] \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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7659--7659 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7662--7662 [] \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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7938--7938 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7939--7939 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7945--7945 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7947--7947 []\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] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2164--2166 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2166--2168 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2168--2170 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , [3373] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2170--2172 []| \T1/pcr/m/n/10 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paragraph at lines 2731--2733 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2733--2735 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2735--2737 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3379] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2865--2867 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] Overfull \hbox (62.8567pt too wide) in paragraph at lines 3810--3812 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3812--3814 []\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3814--3816 []\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method Overfull \hbox (20.8567pt too wide) 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cbind2,sparseMatrix,sparseMatrix-method [3405] Overfull \hbox (10.01662pt too wide) in paragraph at lines 6648--6650 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3406] [3407] Underfull \vbox (badness 1484) has occurred while \output is active [3408] Overfull \hbox (50.8567pt too wide) in paragraph at lines 7116--7118 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7118--7120 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7120--7122 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7126--7128 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7128--7130 []\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7132--7134 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at lines 7256--7258 []\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method Underfull \vbox (badness 3769) has occurred while \output is active [3410] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7262--7264 []\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7264--7266 []\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7270--7272 []\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7272--7274 []\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7278--7280 []\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7280--7282 []\T1/pcr/m/n/10 coerce,dsCMatrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7282--7284 []\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 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paragraph at lines 7304--7306 []\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7306--7308 []\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7308--7310 []\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7310--7312 []\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7312--7314 []\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7314--7316 []\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7318--7320 []\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7320--7322 []\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7322--7324 []\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7324--7326 []\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7326--7328 []\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7328--7330 []\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7332--7334 []\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7334--7336 []\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7336--7338 []\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7338--7340 []\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7340--7342 []\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7342--7344 []\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7346--7348 []\T1/pcr/m/n/10 coerce,dtCMatrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7348--7350 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7350--7352 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7352--7354 []\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7354--7356 []\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7356--7358 []\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7358--7360 []\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method Overfull 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[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7408--7410 []\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7410--7412 []\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7412--7414 []\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7414--7416 []\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7416--7418 []\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7418--7420 []\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7422--7424 []\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7426--7428 []\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7430--7432 []\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7432--7434 []\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7436--7438 []\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7438--7440 []\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7444--7446 []\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7446--7448 []\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7448--7450 []\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7450--7452 []\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7452--7454 []\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7454--7456 []\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7456--7458 []\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7458--7460 []\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7460--7462 []\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method Underfull \vbox (badness 3769) has occurred while \output is active [3412] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7462--7464 []\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7464--7466 []\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7466--7468 []\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7468--7470 []\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7470--7472 []\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7474--7476 []\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7476--7478 []\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7478--7480 []\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7480--7482 []\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7482--7484 []\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7484--7486 []\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7486--7488 []\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7490--7492 []\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7492--7494 []\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7494--7496 []\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7496--7498 []\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7498--7500 []\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7500--7502 []\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7504--7506 []\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7506--7508 []\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7518--7520 []\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7520--7522 []\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7522--7524 []\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7524--7526 []\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7526--7528 []\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7528--7530 []\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7532--7534 []\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7534--7536 []\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7536--7538 []\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7538--7540 []\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method Underfull \vbox (badness 6876) has occurred while \output is active [3413] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7540--7542 []\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7542--7544 []\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7544--7546 []\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7546--7548 []\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7548--7550 []\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7550--7552 []\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7554--7556 []\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7556--7558 []\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7558--7560 []\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7562--7564 []\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7564--7566 []\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7566--7568 []\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7570--7572 []\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7572--7574 []\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7574--7576 []\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7576--7578 []\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7578--7580 []\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 7580--7582 []\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7582--7584 []\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7584--7586 []\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7586--7588 []\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7588--7590 []\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7590--7592 []\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7592--7594 []\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7602--7604 []\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7604--7606 []\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7606--7608 []\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7616--7618 []\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7618--7620 []\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method Underfull \vbox (badness 5022) has occurred while \output is active [3414] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7648--7650 []\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7678--7680 []\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7704--7706 []\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7706--7708 []\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7708--7710 []\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7710--7712 []\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7712--7714 []\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active [3415] Overfull \hbox (14.8567pt too wide) in paragraph at lines 7714--7716 []\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7718--7720 []\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7720--7722 []\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7722--7724 []\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7726--7728 []\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7728--7730 []\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7730--7732 []\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7734--7736 []\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7736--7738 []\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7738--7740 []\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7740--7742 []\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7744--7746 []\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7746--7748 []\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7748--7750 []\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7750--7752 []\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7752--7754 []\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7754--7756 []\T1/pcr/m/n/10 coerce,ndenseMatrix,nsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7756--7758 []\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7758--7760 []\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7760--7762 []\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method Underfull \vbox (badness 2903) has occurred while \output is active Overfull \hbox (32.8567pt too wide) in paragraph at lines 7764--7766 []\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7766--7768 []\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7770--7772 []\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7774--7776 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7776--7778 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7778--7780 []\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7780--7782 []\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7782--7784 []\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7786--7788 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7788--7790 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7790--7792 []\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7792--7794 []\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7794--7796 []\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7796--7798 []\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7798--7800 []\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7800--7802 []\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active [3416] Overfull \hbox (32.8567pt too wide) in paragraph at lines 7804--7806 []\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7806--7808 []\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7808--7810 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7810--7812 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7816--7818 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7818--7820 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7820--7822 []\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7822--7824 []\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 7824--7826 []\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7838--7840 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7840--7842 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7842--7844 []\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7846--7848 []\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7848--7850 []\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7852--7854 []\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7854--7856 []\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7856--7858 []\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7858--7860 []\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7880--7882 []\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method [3417] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7882--7884 []\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7884--7886 []\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7886--7888 []\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7888--7890 []\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7890--7892 []\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7892--7894 []\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7896--7898 []\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7898--7900 []\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7902--7904 []\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7904--7906 []\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7908--7910 []\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7910--7912 []\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7912--7914 []\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7914--7916 []\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7916--7918 []\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 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paragraph at lines 7936--7938 []\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7938--7940 []\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7940--7942 []\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7944--7946 []\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7952--7954 []\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7958--7960 []\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7962--7964 []\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active [3418] Overfull \hbox (20.8567pt too wide) in paragraph at lines 7966--7968 []\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7978--7980 []\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7980--7982 []\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7982--7984 []\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7984--7986 []\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7986--7988 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7988--7990 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7990--7992 []\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7992--7994 []\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 7994--7996 []\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7996--7998 []\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7998--8000 []\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8000--8002 []\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8002--8004 []\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8004--8006 []\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8010--8012 []\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8012--8014 []\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8014--8016 []\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8016--8018 []\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8018--8020 []\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8020--8022 []\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8022--8024 []\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8024--8026 []\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8026--8028 []\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8028--8030 []\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8030--8032 []\T1/pcr/m/n/10 coerce,sparseVector,integer-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8032--8034 []\T1/pcr/m/n/10 coerce,sparseVector,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8034--8036 []\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8036--8038 []\T1/pcr/m/n/10 coerce,sparseVector,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8038--8040 []\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8040--8042 []\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8042--8044 []\T1/pcr/m/n/10 coerce,sparseVector,vector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8044--8046 []\T1/pcr/m/n/10 coerce,table,sparseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8046--8048 []\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8048--8050 []\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8050--8052 []\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8052--8054 []\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8054--8056 []\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8056--8058 []\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8058--8060 []\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8060--8062 []\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8062--8064 []\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8064--8066 []\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8066--8068 []\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method Underfull \vbox (badness 2903) has occurred while \output is active [3419] Overfull \hbox (56.8567pt too wide) in paragraph at lines 8068--8070 []\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8070--8072 []\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8072--8074 []\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8204--8206 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8210--8212 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Underfull \vbox (badness 1117) has occurred while \output is active [3420] Overfull \hbox (62.8567pt too wide) in paragraph at lines 8222--8224 []\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8224--8226 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8238--8240 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3421] [3422] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 8736--8738 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8738--8740 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 8740--8742 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8742--8744 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8744--8746 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8746--8748 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 8748--8750 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8750--8752 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,ddenseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8752--8754 []\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 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(\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3439] Overfull \hbox (20.8567pt too wide) in paragraph at lines 12100--12102 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [3440] [3441] [3442] [3443] Overfull \hbox (8.8567pt too wide) in paragraph at lines 12819--12821 []\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12821--12823 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12829--12831 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method [3444] Overfull \hbox (2.8567pt too wide) in paragraph at lines 12990--12992 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12996--12998 []\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12998--13000 []\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method Overfull \hbox (8.8567pt 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paragraph at lines 13118--13120 []\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method Underfull \vbox (badness 2564) has occurred while \output is active Overfull \hbox (20.8567pt too wide) in paragraph at lines 13209--13211 []\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13213--13215 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13215--13217 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13217--13219 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method [3446] Overfull \hbox (20.8567pt too wide) in paragraph at lines 13219--13221 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13221--13223 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13223--13225 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13225--13227 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13227--13229 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13229--13231 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13233--13235 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13235--13237 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13237--13239 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13239--13241 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13241--13243 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3447] [3448] [3449] Overfull \hbox (50.8567pt too wide) in paragraph at lines 13965--13967 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13971--13973 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 13973--13975 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13975--13977 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13977--13979 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13979--13981 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Underfull \vbox (badness 1348) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 13985--13987 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 13995--13997 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 13997--13999 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 13999--14001 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 14001--14003 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14003--14005 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14011--14013 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14021--14023 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 14023--14025 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Underfull \vbox (badness 3302) has occurred while \output is active [3450] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14031--14033 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14033--14035 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14035--14037 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14037--14039 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14039--14041 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3451] [3452] [3453] [3454] Overfull \hbox (52.01662pt too wide) in paragraph at lines 14973--14975 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3455] [3456] Overfull \hbox (8.8567pt too wide) in paragraph at lines 15491--15493 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 15510--15512 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15512--15514 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15518--15520 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Underfull \vbox (badness 1019) has occurred while \output is active [3457] Overfull \hbox (14.8567pt too wide) in paragraph at lines 15536--15538 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15542--15544 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15544--15546 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3458] Overfull \hbox (26.8567pt too wide) in paragraph at lines 15783--15785 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15789--15791 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15801--15803 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15803--15805 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 15805--15807 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15807--15809 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 15809--15811 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method Underfull \vbox (badness 6876) has occurred while \output is active [3459] Overfull \hbox (38.8567pt too wide) in paragraph at lines 15829--15831 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15831--15833 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15847--15849 []\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (38.8567pt too wide) in paragraph at lines 15867--15869 []\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15869--15871 []\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15887--15889 []\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15895--15897 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method [3460] Overfull \hbox (38.8567pt too wide) in paragraph at lines 15899--15901 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15901--15903 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15903--15905 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15921--15923 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15923--15925 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15925--15927 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15927--15929 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15931--15933 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15935--15937 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15939--15941 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3461] Overfull \hbox (46.01662pt too wide) in paragraph at lines 16125--16127 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3462] [3463] [3464] [3465] [3466] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17382--17384 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17385--17387 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17387--17389 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17389--17391 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17391--17393 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17393--17395 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 17395--17397 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3467] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17397--17399 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17399--17401 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17401--17403 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 17405--17407 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17407--17409 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17409--17411 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17411--17413 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17413--17415 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17415--17417 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Underfull \vbox (badness 2564) has occurred while \output is active [3468] [3469] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17752--17754 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17822--17824 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3470] [3471] [3472] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18274--18276 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18283--18285 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18285--18287 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18287--18289 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18289--18291 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18301--18303 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18311--18313 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 18326--18328 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18332--18334 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3473] [3474] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18638--18640 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18640--18642 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18642--18644 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18644--18646 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 18648--18650 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18650--18652 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18652--18654 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18654--18656 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 18656--18658 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18658--18660 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 18660--18662 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18666--18668 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18670--18672 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18680--18682 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18684--18686 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18686--18688 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18688--18690 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 18690--18692 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18692--18694 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18694--18696 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 18696--18698 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18725--18727 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18727--18729 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 18729--18731 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18731--18733 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method [3475] Overfull \hbox (2.8567pt too wide) in paragraph at lines 18735--18737 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18739--18741 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18743--18745 []\T1/pcr/m/n/10 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/usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb> Output written on fullrefman.pdf (3554 pages, 9691795 bytes). Transcript written on fullrefman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. Chapter 2 [1] [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (49 pages, 363015 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 379968 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex) [1{/usr/sh are/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 379968 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/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-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] Chapter 1 [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] 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] Overfull \hbox (29.11234pt too wide) in paragraph at lines 2213--2224 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3199--3199 []@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] Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 @textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A []rn-Helge [54] [55] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4803--4803 []@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] (Concept index) [68] (Environment variable index) [69] [70] ) (see the transcript file for additional information) Output written on R-admin.pdf (73 pages, 448601 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/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 (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] 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] Overfull \hbox (29.11234pt too wide) in paragraph at lines 2213--2224 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3199--3199 []@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] Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 @textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A []rn-Helge [54] [55] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4803--4803 []@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) 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) restricted \write18 enabled. 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 (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] 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] Overfull \hbox (29.11234pt too wide) in paragraph at lines 2213--2224 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3199--3199 []@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] Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % Underfull \hbox (badness 10000) in paragraph at lines 4660--4664 @textrm https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html Bj[]A []rn-Helge [54] [55] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4803--4803 []@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) 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) restricted \write18 enabled. 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) Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@textbf xlsReadWrite[][]| 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) Output written on R-data.pdf (33 pages, 265090 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/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) Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@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) 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) restricted \write18 enabled. 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) Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@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) Output written on R-data.pdf (35 pages, 304306 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/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) Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@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) Output written on R-data.pdf (35 pages, 304306 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] (Acknowledgements) Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 6296--6302 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82] Chapter 4 [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [88] [89] [90] [91] Overfull \hbox (56.55324pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [92] Underfull \hbox (badness 10000) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt - [93] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (16.31242pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [110] [111] [112] [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [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] Underfull \hbox (badness 10000) in paragraph at lines 13022--13028 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [156] Overfull \hbox (33.55849pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 13990--13997 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [163] [164] (Function and variable index) [165] (Concept index) [166] [167] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb > Output written on R-exts.pdf (170 pages, 839651 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 6296--6302 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82] Chapter 4 [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [88] [89] [90] [91] Overfull \hbox (56.55324pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [92] Underfull \hbox (badness 10000) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt - [93] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (16.31242pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [110] [111] [112] [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [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] Underfull \hbox (badness 10000) in paragraph at lines 13022--13028 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [156] Overfull \hbox (33.55849pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 13990--13997 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [163] [164] (Function and variable index) [165] (./R-exts.vrs [166] [167]) (Concept index) [168] (./R-exts.cps [169]) [170] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb> Output written on R-exts.pdf (176 pages, 902612 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 6296--6302 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82] Chapter 4 [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [88] [89] [90] [91] Overfull \hbox (56.55324pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [92] Underfull \hbox (badness 10000) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt - [93] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (16.31242pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [110] [111] [112] [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [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] Underfull \hbox (badness 10000) in paragraph at lines 13022--13028 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [156] Overfull \hbox (33.55849pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 13990--13997 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [163] [164] (Function and variable index) [165] (./R-exts.vrs [166] [167]) (Concept index) [168] (./R-exts.cps [169]) [170] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb> Output written on R-exts.pdf (176 pages, 902609 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Chapter 2 [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 6296--6302 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [71] [72] [73] [74] Chapter 3 [75] [76] [77] [78] [79] [80] [81] [82] Chapter 4 [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [88] [89] [90] [91] Overfull \hbox (56.55324pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [92] Underfull \hbox (badness 10000) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt - [93] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [94] [95] [96] [97] Chapter 5 [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (16.31242pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [110] [111] [112] [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [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] Underfull \hbox (badness 10000) in paragraph at lines 13022--13028 []@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] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [156] Overfull \hbox (33.55849pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [157] [158] [159] [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 13990--13997 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [163] [164] (Function and variable index) [165] (./R-exts.vrs [166] [167]) (Concept index) [168] (./R-exts.cps [169]) [170] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb> Output written on R-exts.pdf (176 pages, 902609 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6650--6655 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] Appendix E [94] Appendix F [95] [96] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb> Output written on R-intro.pdf (99 pages, 585875 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6650--6655 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] (./R-intro.vrs [94] [95]) Appendix E [96] (./R-intro.cps [97]) Appendix F [98] [99] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on R-intro.pdf (105 pages, 636736 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p df> [35] [36] <./images/ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6650--6655 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] (./R-intro.vrs [94] [95]) Appendix E [96] (./R-intro.cps [97]) Appendix F [98] [99] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on R-intro.pdf (105 pages, 636733 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [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] Underfull \hbox (badness 10000) in paragraph at lines 3838--3843 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [46] [47] [48] [49] Chapter 9 [50] [51] Chapter 10 [52] Chapter 11 [53] Chapter 12 [54] [55] (Function and variable index) [56] (Concept index) [57] [58] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on R-ints.pdf (61 pages, 385262 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [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] Underfull \hbox (badness 10000) in paragraph at lines 3838--3843 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [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]) (Concept index) [58] (./R-ints.cps) [59] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on R-ints.pdf (63 pages, 433537 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [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] Underfull \hbox (badness 10000) in paragraph at lines 3838--3843 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [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]) (Concept index) [58] (./R-ints.cps) [59] ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/cm-super/cm-super-t1.enc} Output written on R-ints.pdf (63 pages, 433543 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.3.0/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-defs.texi (/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex)) (./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] Chapter 1 Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 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] (Concept Index) [52] Appendix A [53] [54] ) (see the transcript file for additional information) Output written on R-lang.pdf (57 pages, 327172 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) 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) 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) 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' make[1]: Nothing to be done for `install'. 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 `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 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' 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 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' 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 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/00Index.html + for i in '$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' 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-i '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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/anova.negbin.html + for i in 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/gamma.shape.glm.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/logtrans.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/quine.html + for i in '$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 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i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/MASS/html/steam.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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/BunchKaufman-methods.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/CAex.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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/CHMfactor-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/Cholesky-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/MatrixFactorization-class.html + for i in '$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-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/Schur-class.html + for i in '$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/Schur.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/abIndex-class.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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/abIseq.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/all-methods.html + for i in '$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/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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/bandSparse.html + for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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' 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'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 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for i in '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/dtpMatrix-class.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/graph2T.html + for i in '$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' 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/lsyMatrix-class.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/norm.html + for i in '$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' 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'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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/Matrix/html/unused-classes.html + for i in '$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' 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's|\..\/\..\/..\/doc|/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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/La_version.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/Recall.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/base/html/weekday.POSIXt.html + for i in '$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' 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-i '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' 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'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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/frame.html + for i in '$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' 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'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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/graphics/html/plot.window.html + for i in '$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' 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'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' 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'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 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/mgcv/html/mgcv-FAQ.html + for i in '$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 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Dim.corStruct.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Gun.html + for i in '$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' 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's|\..\/\..\/..\/doc|/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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nlme/html/Oxide.html + for i in '$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 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/nnet/html/nnet.Hess.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i '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' 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/rpart/html/post.rpart.html + for i in '$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 '$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' 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's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats/html/interaction.plot.html + for i in '$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' 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's|\..\/\..\/..\/doc|/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 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'$RPM_BUILD_ROOT/usr/lib/R/library/*/html/*.html' + sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.3.0|g' /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/library/stats4/html/mle.html + for i in '$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 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+ sed -i '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' 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+ 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 extracting debug info from /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/bin/Rscript extracting debug info from /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/libRmath.so extracting debug info from /builddir/build/BUILDROOT/R-3.3.0-3.el7.arm/usr/lib/R/bin/Rscript *** WARNING: identical binaries are copied, not linked: /usr/lib/R/bin/Rscript and /usr/bin/Rscript extracting debug info from 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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