Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/f31-build-51297-27496/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1563667200 Wrote: /builddir/build/SRPMS/R-3.6.0-3.fc31.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/f31-build-51297-27496/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1563667200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lQyMM3 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf R-3.6.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/R-3.6.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd R-3.6.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .fixpath --fuzz=0 + cat + chmod +x /builddir/build/BUILD/R-3.6.0/R-prov + cat + chmod +x /builddir/build/BUILD/R-3.6.0/R-req + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch): patching file src/scripts/javareconf.in Hunk #1 succeeded at 79 (offset 1 line). Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.cTasl6 + umask 022 + cd /builddir/build/BUILD + cd R-3.6.0 + echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library'\''}' + 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 "riscv64" 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + export 'FFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' BUILDSTDERR: +++ dirname ./configure BUILDSTDERR: ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./tools/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./tools/config.guess BUILDSTDERR: ++ basename ./tools/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./tools/config.guess + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./tools/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./tools/config.sub BUILDSTDERR: ++ basename ./tools/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./tools/config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' BUILDSTDERR: ++ find . -name ltmain.sh + for i in $(find . -name ltmain.sh) + /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./tools/ltmain.sh + ./configure --build=riscv64-koji-linux-gnu --host=riscv64-koji-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/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-system-tre --with-system-valgrind-headers --with-lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh --enable-BLAS-shlib --enable-R-shlib --enable-prebuilt-html --enable-memory-profiling MAKEINFO=texi2any rdocdir=/usr/share/doc/R rincludedir=/usr/include/R rsharedir=/usr/share/R BUILDSTDERR: configure: WARNING: unrecognized options: --disable-dependency-tracking BUILDSTDERR: ./configure: line 18793: cd: /lib64/lp64d/../lib64/lp64d: No such file or directory BUILDSTDERR: ./configure: line 18793: cd: /usr/lib64/lp64d/../lib64/lp64d: No such file or directory BUILDSTDERR: ./configure: line 18821: cd: /lib64/lp64d/../lib64/lp64d: No such file or directory BUILDSTDERR: ./configure: line 18821: cd: /usr/lib64/lp64d/../lib64/lp64d: No such file or directory BUILDSTDERR: ./configure: line 20184: ::: command not found BUILDSTDERR: ./configure: line 38740: cd: /lib64/lp64d/../lib64/lp64d/: No such file or directory BUILDSTDERR: ./configure: line 38740: cd: /usr/lib64/lp64d/../lib64/lp64d/: No such file or directory BUILDSTDERR: configure: WARNING: unrecognized options: --disable-dependency-tracking + cat CONFIGURE.log + grep -A30 'R is now' - + make V=1 BUILDSTDERR: blas.f:1614:0: BUILDSTDERR: 1614 | DH22=DH22*GAM BUILDSTDERR: | BUILDSTDERR: Warning: 'dh22' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:1613:0: BUILDSTDERR: 1613 | DH21=DH21*GAM BUILDSTDERR: | BUILDSTDERR: Warning: 'dh21' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:1480:0: BUILDSTDERR: 1480 | 1 DQ2,DU,DY1,ZERO,GAMSQ,DD1,DFLAG,DH12,DH22,DP1,DQ1, BUILDSTDERR: | BUILDSTDERR: Warning: 'dh12' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:1590:0: BUILDSTDERR: 1590 | DH11=DH11*GAM BUILDSTDERR: | BUILDSTDERR: Warning: 'dh11' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:2409:0: BUILDSTDERR: 2409 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:2618:0: BUILDSTDERR: 2618 | INTEGER I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY BUILDSTDERR: | BUILDSTDERR: Warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:2618:0: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:2618:0: Warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:2618:0: Warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:3451:0: BUILDSTDERR: 3451 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:3659:0: BUILDSTDERR: 3659 | INTEGER I, INFO, IX, IY, J, JX, JY, KX, KY BUILDSTDERR: | BUILDSTDERR: Warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:3659:0: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:3659:0: Warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:3659:0: Warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:4550:0: BUILDSTDERR: 4550 | INTEGER I, INFO, IX, J, JX, KPLUS1, KX, L BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:4896:0: BUILDSTDERR: 4896 | INTEGER I, INFO, IX, J, JX, KPLUS1, KX, L BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:5198:0: BUILDSTDERR: 5198 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:5500:0: BUILDSTDERR: 5500 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:6157:0: BUILDSTDERR: 6157 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: blas.f:6824:0: BUILDSTDERR: 6824 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:4796:26: BUILDSTDERR: 4796 | RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplxblas.f:4808:26: BUILDSTDERR: 4808 | RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplxblas.f:1130:0: BUILDSTDERR: 1130 | INTEGER I, INFO, IX, IY, J, JX, JY, KX, KY BUILDSTDERR: | BUILDSTDERR: Warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:1130:0: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:1130:0: Warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:1130:0: Warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:2208:0: BUILDSTDERR: 2208 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:2946:0: BUILDSTDERR: 2946 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:4386:0: BUILDSTDERR: 4386 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:5195:0: BUILDSTDERR: 5195 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:5423:0: BUILDSTDERR: 5423 | INTEGER I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY BUILDSTDERR: | BUILDSTDERR: Warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:5423:0: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:5423:0: Warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:5423:0: Warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:6649:0: BUILDSTDERR: 6649 | INTEGER I, INFO, IX, J, JX, KPLUS1, KX, L BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:7030:0: BUILDSTDERR: 7030 | INTEGER I, INFO, IX, J, JX, KPLUS1, KX, L BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:7367:0: BUILDSTDERR: 7367 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplxblas.f:7708:0: BUILDSTDERR: 7708 | INTEGER I, INFO, IX, J, JX, K, KK, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/m4' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/m4' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/tools' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/tools' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/html' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/html' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/etc' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/etc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/share' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/share' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/scripts' creating src/scripts/R.fe make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/scripts' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/scripts' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include' mkdir -p -- ../../include make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include/R_ext' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c blas.f -o blas.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c cmplxblas.f -o cmplxblas.o gcc -shared -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libRblas.so blas.o cmplxblas.o -L -L -lgfortran -lm make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' mkdir -p -- /builddir/build/BUILD/R-3.6.0/lib make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' making xdr.d from xdr.c making xdr_float.d from xdr_float.c making xdr_mem.d from xdr_mem.c making xdr_stdio.d from xdr_stdio.c make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c xdr.c -o xdr.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c xdr_float.c -o xdr_float.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o ar -cr libxdr.a xdr.o xdr_float.o xdr_mem.o xdr_stdio.o ranlib libxdr.a make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/appl' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c integrate.c -o integrate.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c interv.c -o interv.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c maxcol.c -o maxcol.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c optim.c -o optim.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pretty.c -o pretty.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c uncmin.c -o uncmin.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dchdc.f -o dchdc.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dpbfa.f -o dpbfa.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dpbsl.f -o dpbsl.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dpoco.f -o dpoco.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dpodi.f -o dpodi.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dpofa.f -o dpofa.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dposl.f -o dposl.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dqrdc.f -o dqrdc.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dqrdc2.f -o dqrdc2.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dqrls.f -o dqrls.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dqrsl.f -o dqrsl.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dqrutl.f -o dqrutl.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dsvdc.f -o dsvdc.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dtrco.f -o dtrco.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dtrsl.f -o dtrsl.o ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/appl' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/appl' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mlutils.c -o mlutils.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c d1mach.c -o d1mach.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c i1mach.c -o i1mach.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmax2.c -o fmax2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmin2.c -o fmin2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fprec.c -o fprec.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fround.c -o fround.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ftrunc.c -o ftrunc.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sign.c -o sign.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fsign.c -o fsign.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imax2.c -o imax2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imin2.c -o imin2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chebyshev.c -o chebyshev.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c log1p.c -o log1p.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgammacor.c -o lgammacor.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gammalims.c -o gammalims.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stirlerr.c -o stirlerr.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bd0.c -o bd0.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma.c -o gamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgamma.c -o lgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c beta.c -o beta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lbeta.c -o lbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c polygamma.c -o polygamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cospi.c -o cospi.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_i.c -o bessel_i.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_j.c -o bessel_j.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_k.c -o bessel_k.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_y.c -o bessel_y.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c choose.c -o choose.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c snorm.c -o snorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sexp.c -o sexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgamma.c -o dgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgamma.c -o pgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgamma.c -o qgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgamma.c -o rgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbeta.c -o dbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbeta.c -o pbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbeta.c -o qbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbeta.c -o rbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dunif.c -o dunif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c punif.c -o punif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qunif.c -o qunif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c runif.c -o runif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnorm.c -o dnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnorm.c -o pnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnorm.c -o qnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnorm.c -o rnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlnorm.c -o dlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plnorm.c -o plnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlnorm.c -o qlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlnorm.c -o rlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c df.c -o df.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pf.c -o pf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qf.c -o qf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rf.c -o rf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnf.c -o dnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dt.c -o dt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pt.c -o pt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qt.c -o qt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rt.c -o rt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnt.c -o dnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dchisq.c -o dchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pchisq.c -o pchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qchisq.c -o qchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rchisq.c -o rchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnchisq.c -o rnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbinom.c -o dbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbinom.c -o pbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbinom.c -o qbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbinom.c -o rbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rmultinom.c -o rmultinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dcauchy.c -o dcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pcauchy.c -o pcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qcauchy.c -o qcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rcauchy.c -o rcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dexp.c -o dexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pexp.c -o pexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qexp.c -o qexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rexp.c -o rexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgeom.c -o dgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgeom.c -o pgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgeom.c -o qgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgeom.c -o rgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dhyper.c -o dhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c phyper.c -o phyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qhyper.c -o qhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rhyper.c -o rhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbinom.c -o dnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbinom.c -o pnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbinom.c -o qnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnbinom.c -o rnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dpois.c -o dpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ppois.c -o ppois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qpois.c -o qpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpois.c -o rpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dweibull.c -o dweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pweibull.c -o pweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qweibull.c -o qweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rweibull.c -o rweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlogis.c -o dlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plogis.c -o plogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlogis.c -o qlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlogis.c -o rlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnchisq.c -o dnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnchisq.c -o pnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnchisq.c -o qnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbeta.c -o dnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbeta.c -o pnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbeta.c -o qnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnf.c -o pnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnt.c -o pnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnf.c -o qnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnt.c -o qnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ptukey.c -o ptukey.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qtukey.c -o qtukey.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c toms708.c -o toms708.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c wilcox.c -o wilcox.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rembedded.c -o Rembedded.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dynload.c -o dynload.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c system.c -o system.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sys-unix.c -o sys-unix.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sys-std.c -o sys-std.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/unix' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -DR_HOME='"/builddir/build/BUILD/R-3.6.0"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/unix' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/unix' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making altclasses.d from altclasses.c making altrep.d from altrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c CommandLineArgs.c -o CommandLineArgs.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rdynload.c -o Rdynload.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Renviron.c -o Renviron.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c RNG.c -o RNG.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agrep.c -o agrep.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c altclasses.c -o altclasses.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c altrep.c -o altrep.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c apply.c -o apply.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c arithmetic.c -o arithmetic.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c array.c -o array.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c attrib.c -o attrib.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bind.c -o bind.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c builtin.c -o builtin.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c character.c -o character.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coerce.c -o coerce.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c colors.c -o colors.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c complex.c -o complex.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c connections.c -o connections.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c context.c -o context.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cum.c -o cum.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dcf.c -o dcf.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c datetime.c -o datetime.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c debug.c -o debug.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c deparse.c -o deparse.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devices.c -o devices.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dotcode.c -o dotcode.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dounzip.c -o dounzip.o BUILDSTDERR: gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_COIn file included from /usr/include/string.h:494, BUILDSTDERR: from ../../src/include/Rinlinedfuns.h:73, BUILDSTDERR: from ../../src/include/Rinternals.h:1550, BUILDSTDERR: from ../../src/include/Defn.h:81, BUILDSTDERR: from eval.c:27: BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'inflateAssignmentCall' at eval.c:6083:5, BUILDSTDERR: inlined from 'R_getBCInterpreterExpression' at eval.c:6136:8: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: eval.c: In function 'R_getBCInterpreterExpression': BUILDSTDERR: eval.c:6076:19: note: length computed here BUILDSTDERR: 6076 | size_t slen = strlen(name); BUILDSTDERR: | ^~~~~~~~~~~~ NFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dstruct.c -o dstruct.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c duplicate.c -o duplicate.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c edit.c -o edit.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c engine.c -o engine.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c envir.c -o envir.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c errors.c -o errors.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c eval.c -o eval.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c format.c -o format.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gevents.c -o gevents.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gram.c -o gram.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gram-ex.c -o gram-ex.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c graphics.c -o graphics.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c grep.c -o grep.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c identical.c -o identical.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c inlined.c -o inlined.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c inspect.c -o inspect.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c internet.c -o internet.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c iosupport.c -o iosupport.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lapack.c -o lapack.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c list.c -o list.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c localecharset.c -o localecharset.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c logic.c -o logic.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c main.c -o main.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mapply.c -o mapply.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c match.c -o match.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c memory.c -o memory.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c names.c -o names.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c objects.c -o objects.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c options.c -o options.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c paste.c -o paste.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c platform.c -o platform.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plot.c -o plot.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plot3d.c -o plot3d.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plotmath.c -o plotmath.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c print.c -o print.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c printarray.c -o printarray.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c printvector.c -o printvector.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c printutils.c -o printutils.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qsort.c -o qsort.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c radixsort.c -o radixsort.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c random.c -o random.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c raw.c -o raw.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c registration.c -o registration.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c relop.c -o relop.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlocale.c -o rlocale.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c saveload.c -o saveload.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c scan.c -o scan.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c seq.c -o seq.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c serialize.c -o serialize.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sort.c -o sort.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c source.c -o source.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c split.c -o split.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sprintf.c -o sprintf.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c startup.c -o startup.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c subassign.c -o subassign.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c subscript.c -o subscript.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c subset.c -o subset.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c summary.c -o summary.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sysutils.c -o sysutils.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c times.c -o times.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c unique.c -o unique.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c util.c -o util.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c version.c -o version.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c g_alab_her.c -o g_alab_her.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c g_cntrlify.c -o g_cntrlify.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c g_fontdb.c -o g_fontdb.o gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c g_her_glyph.c -o g_her_glyph.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c xxxpr.f -o xxxpr.o gcc -shared -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/xdr/libxdr.a -L"../../lib" -lRblas -L -L -lgfortran -lm -lreadline -ltre -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' mkdir -p -- /builddir/build/BUILD/R-3.6.0/bin/exec make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' gcc -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rmain.c -o Rmain.o gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o R.bin Rmain.o -lR -lRblas make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making libcurl.d from libcurl.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c internet.c -o internet.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c libcurl.c -o libcurl.o BUILDSTDERR: gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-sdlapack.f:6871:19: BUILDSTDERR: 6871 | K = SCALE( I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:6885:19: BUILDSTDERR: 6885 | K = SCALE( I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:9161:21: BUILDSTDERR: 9161 | HSWORK = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:9776:21: BUILDSTDERR: 9776 | HSWORK = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16788:28: BUILDSTDERR: 16788 | LWORK_DGEQRF=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16792:28: BUILDSTDERR: 16792 | LWORK_DORMQR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16807:28: BUILDSTDERR: 16807 | LWORK_DGEBRD=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16811:28: BUILDSTDERR: 16811 | LWORK_DORMBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:98487:18: BUILDSTDERR: 98487 | LWKOPT = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16815:28: BUILDSTDERR: 16815 | LWORK_DORGBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16839:31: BUILDSTDERR: 16839 | LWORK_DGELQF=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16843:31: BUILDSTDERR: 16843 | LWORK_DGEBRD=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16847:31: BUILDSTDERR: 16847 | LWORK_DORMBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16851:31: BUILDSTDERR: 16851 | LWORK_DORGBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16855:31: BUILDSTDERR: 16855 | LWORK_DORMLQ=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16875:31: BUILDSTDERR: 16875 | LWORK_DGEBRD=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16879:31: BUILDSTDERR: 16879 | LWORK_DORMBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:16883:31: BUILDSTDERR: 16883 | LWORK_DORGBR=DUM(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:36428:13: BUILDSTDERR: 36428 | LOPT = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:35370:13: BUILDSTDERR: 35370 | LOPT = WORK( M+NP+1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:36726:13: BUILDSTDERR: 36726 | LOPT = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:36074:13: BUILDSTDERR: 36074 | LOPT = WORK( P+MN+1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:124156:14: BUILDSTDERR: 124156 | LWMIN = MAX( DBLE( LWMIN ), DBLE( WORK( 1 ) ) ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:124157:15: BUILDSTDERR: 124157 | LIWMIN = MAX( DBLE( LIWMIN ), DBLE( IWORK( 1 ) ) ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:136875:13: BUILDSTDERR: 136875 | LOPT = MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:136876:14: BUILDSTDERR: 136876 | LIOPT = MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:138054:21: BUILDSTDERR: 138054 | LWKOPT = WORK(1) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: dlapack.f:77843:34: BUILDSTDERR: 77843 | SUBROUTINE DLARRV( N, VL, VU, D, L, PIVMIN, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'vu' at (1) [-Wunused-dummy-argument] BUILDSTDERR: dlapack.f:74326:54: BUILDSTDERR: 74326 | SUBROUTINE DLARRC( JOBT, N, VL, VU, D, E, PIVMIN, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'pivmin' at (1) [-Wunused-dummy-argument] BUILDSTDERR: dlapack.f:46267:45: BUILDSTDERR: 46267 | $ RELTOL, PIVMIN, D, E, E2, NVAL, AB, C, MOUT, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'e' at (1) [-Wunused-dummy-argument] BUILDSTDERR: dlapack.f:58693:55: BUILDSTDERR: 58693 | INTEGER FUNCTION DLANEG( N, D, LLD, SIGMA, PIVMIN, R ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'pivmin' at (1) [-Wunused-dummy-argument] BUILDSTDERR: SRC/iparam2stage.F:612:68: BUILDSTDERR: Warning: Unused dummy argument 'lwork' at (1) [-Wunused-dummy-argument] BUILDSTDERR: SRC/iparam2stage.F:612:51: BUILDSTDERR: Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument] BUILDSTDERR: SRC/iparam2stage.F:612:48: BUILDSTDERR: Warning: Unused dummy argument 'opts' at (1) [-Wunused-dummy-argument] BUILDSTDERR: dlapack.f:128949:23: BUILDSTDERR: 128949 | $ ABSTOL, M, W, Z, LDZ, ISUPPZ, WORK, LWORK, IWORK, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'abstol' at (1) [-Wunused-dummy-argument] BUILDSTDERR: dlapack.f:95122:0: BUILDSTDERR: 95122 | X( J ) = X( J ) / TJJS - SUMJ BUILDSTDERR: | BUILDSTDERR: Warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:93997:0: BUILDSTDERR: 93997 | X( J ) = X( J ) / TJJS - SUMJ BUILDSTDERR: | BUILDSTDERR: Warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:92881:0: BUILDSTDERR: 92881 | X( J ) = X( J ) / TJJS - SUMJ BUILDSTDERR: | BUILDSTDERR: Warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:126561:0: BUILDSTDERR: 126561 | IPIV( K ) = KP BUILDSTDERR: | BUILDSTDERR: Warning: 'kp' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:126255:0: BUILDSTDERR: 126255 | ELSE IF( ABS( AP( KPC+IMAX-1 ) ).GE.ALPHA*ROWMAX ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:155012:0: BUILDSTDERR: 155012 | $ AP( JCLAST ), AP( JC+1 ), 1 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'jclast' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:79873:0: BUILDSTDERR: 79873 | ISEED( 4 ) = IT4 BUILDSTDERR: | BUILDSTDERR: Warning: 'it4' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:79872:0: BUILDSTDERR: 79872 | ISEED( 3 ) = IT3 BUILDSTDERR: | BUILDSTDERR: Warning: 'it3' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:79871:0: BUILDSTDERR: 79871 | ISEED( 2 ) = IT2 BUILDSTDERR: | BUILDSTDERR: Warning: 'it2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:79870:0: BUILDSTDERR: 79870 | ISEED( 1 ) = IT1 BUILDSTDERR: | BUILDSTDERR: Warning: 'it1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:129396:0: BUILDSTDERR: 129396 | IF( NRM.LT.DTPCRT ) BUILDSTDERR: | BUILDSTDERR: Warning: 'dtpcrt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:129187:0: BUILDSTDERR: 129187 | INTEGER B1, BLKSIZ, BN, GPIND, I, IINFO, INDRV1, BUILDSTDERR: | BUILDSTDERR: Warning: 'gpind' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:129362:0: BUILDSTDERR: 129362 | $ ABS( WORK( INDRV1+JMAX ) ) BUILDSTDERR: | BUILDSTDERR: Warning: 'onenrm' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:129376:0: BUILDSTDERR: 129376 | IF( ABS( XJ-XJM ).GT.ORTOL ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ortol' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:129376:0: Warning: 'xjm' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:49708:0: BUILDSTDERR: 49708 | $ TAU = TAU*SCLINV BUILDSTDERR: | BUILDSTDERR: Warning: 'sclinv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:30048:0: BUILDSTDERR: 30048 | A( N, N ) = SMIN BUILDSTDERR: | BUILDSTDERR: Warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:30030:0: BUILDSTDERR: 30030 | $ CALL DSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:30024:0: BUILDSTDERR: 30024 | $ CALL DSWAP( N, A( IPV, 1 ), LDA, A( I, 1 ), LDA ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:91211:0: BUILDSTDERR: 91211 | JPIV( I ) = JPSV BUILDSTDERR: | BUILDSTDERR: Warning: 'jpsv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:91204:0: BUILDSTDERR: 91204 | CALL DSWAP( 4, T16( IPSV, 1 ), 4, T16( I, 1 ), 4 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ipsv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:147008:0: BUILDSTDERR: 147008 | IF( ILBACK ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:88702:0: BUILDSTDERR: 88702 | TAU = S BUILDSTDERR: | BUILDSTDERR: Warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:139541:0: BUILDSTDERR: 139541 | $ CALL DSWAP( N-KP, A( KP+1, KK ), 1, A( KP+1, KP ), 1 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:57295:0: BUILDSTDERR: 57295 | $ DIFRJ ) / ( POLES( I, 2 )+DJ ) BUILDSTDERR: | BUILDSTDERR: Warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:85755:0: BUILDSTDERR: 85755 | $ / ( DSIGMA( I )+DJ ) BUILDSTDERR: | BUILDSTDERR: Warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:62441:0: BUILDSTDERR: 62441 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:62069:0: BUILDSTDERR: 62069 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:61724:0: BUILDSTDERR: 61724 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:61464:0: BUILDSTDERR: 61464 | DOUBLE PRECISION ABSA, SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:61256:0: BUILDSTDERR: 61256 | DOUBLE PRECISION ANORM, SCALE, SUM BUILDSTDERR: | BUILDSTDERR: Warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:61009:0: BUILDSTDERR: 61009 | DOUBLE PRECISION ABSA, SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:59803:0: BUILDSTDERR: 59803 | DOUBLE PRECISION ABSA, SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:55512:0: BUILDSTDERR: 55512 | A( K+NB, NB ) = EI BUILDSTDERR: | BUILDSTDERR: Warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:50392:0: BUILDSTDERR: 50392 | INTEGER I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2 BUILDSTDERR: | BUILDSTDERR: Warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:47548:0: BUILDSTDERR: 47548 | $ N2, NJ, PJ BUILDSTDERR: | BUILDSTDERR: Warning: 'pj' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:55186:0: BUILDSTDERR: 55186 | $ CS, SN ) BUILDSTDERR: | BUILDSTDERR: Warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:85161:0: BUILDSTDERR: 85161 | INTEGER I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M, N, BUILDSTDERR: | BUILDSTDERR: Warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:82313:0: BUILDSTDERR: 82313 | INTEGER CT, I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M, BUILDSTDERR: | BUILDSTDERR: Warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:59577:0: BUILDSTDERR: 59577 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:43147:0: BUILDSTDERR: 43147 | IF( ILZ ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:42638:0: BUILDSTDERR: 42638 | IF( ILQ ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:42516:0: BUILDSTDERR: 42516 | IF( .NOT.ILSCHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:59367:0: BUILDSTDERR: 59367 | DOUBLE PRECISION ANORM, SCALE, SUM, TEMP BUILDSTDERR: | BUILDSTDERR: Warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:59164:0: BUILDSTDERR: 59164 | DOUBLE PRECISION SCALE, SUM, VALUE, TEMP BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:159919:0: BUILDSTDERR: 159919 | WORK( 1 ) = LWMIN BUILDSTDERR: | BUILDSTDERR: Warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:159920:0: BUILDSTDERR: 159920 | IWORK( 1 ) = LIWMIN BUILDSTDERR: | BUILDSTDERR: Warning: 'liwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:58950:0: BUILDSTDERR: 58950 | DOUBLE PRECISION SCALE, SUM, VALUE, TEMP BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: SRC/iparam2stage.F:770:0: BUILDSTDERR: Warning: 'ns' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: SRC/iparam2stage.F:761:0: BUILDSTDERR: Warning: 'nh' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:128102:0: BUILDSTDERR: 128102 | ELSE IF( W( JE ).GE.WUL .AND. IDISCU.GT.0 ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wul' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:128100:0: BUILDSTDERR: 128100 | IF( W( JE ).LE.WLU .AND. IDISCL.GT.0 ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wlu' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46794:0: BUILDSTDERR: 46794 | $ IGIVPT, INDXQ, IPERM, IPRMPT, IQ, IQPTR, IWREM, BUILDSTDERR: | BUILDSTDERR: Warning: 'iwrem' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46921:0: BUILDSTDERR: 46921 | $ INFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'iqptr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46921:0: Warning: 'iq' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46794:0: BUILDSTDERR: 46794 | $ IGIVPT, INDXQ, IPERM, IPRMPT, IQ, IQPTR, IWREM, BUILDSTDERR: | BUILDSTDERR: Warning: 'iprmpt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46794:0: Warning: 'iperm' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46794:0: Warning: 'igivpt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:46793:0: BUILDSTDERR: 46793 | INTEGER CURLVL, CURPRB, CURR, I, IGIVCL, IGIVNM, BUILDSTDERR: | BUILDSTDERR: Warning: 'igivcl' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:102785:0: BUILDSTDERR: 102785 | IF( LWORK.LT.NW*NB+TSIZE ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:99539:0: BUILDSTDERR: 99539 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:135615:0: BUILDSTDERR: 135615 | WORK( 1 ) = LWKOPT BUILDSTDERR: | BUILDSTDERR: Warning: 'lwkopt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:75191:0: BUILDSTDERR: 75191 | IF( W( JE ).GE.WUL .AND. IDISCU.GT.0 ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wul' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:75174:0: BUILDSTDERR: 75174 | IF( W( JE ).LE.WLU .AND. IDISCL.GT.0 ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wlu' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:75712:0: BUILDSTDERR: 75712 | $ ((IRANGE.EQ.VALRNG).AND.(D(1).GT.VL).AND.(D(1).LE.VU)).OR. BUILDSTDERR: | BUILDSTDERR: Warning: 'irange' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:75997:0: BUILDSTDERR: 75997 | CLWDTH = W(WEND) + WERR(WEND) - W(WBEGIN) - WERR(WBEGIN) BUILDSTDERR: | BUILDSTDERR: Warning: 'wend' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:75953:0: BUILDSTDERR: 75953 | IF(MB.EQ.1) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'mb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:104042:0: BUILDSTDERR: 104042 | IF( LWORK.LT.NW*NB+TSIZE ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:22115:0: BUILDSTDERR: 22115 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:152216:0: BUILDSTDERR: 152216 | SCALE = SCALE2 BUILDSTDERR: | BUILDSTDERR: Warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:150508:0: BUILDSTDERR: 150508 | DIF( KS ) = COND BUILDSTDERR: | BUILDSTDERR: Warning: 'cond' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: BUILDSTDERR: 1544 | $ WORK( WSTART ), IWORK, INFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'poles' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'ivt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'is' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'ic' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'givnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'givcol' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'difr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:1544:0: Warning: 'difl' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:104412:0: BUILDSTDERR: 104412 | IF( LWORK.LT.NW*NB+TSIZE ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:163493:0: BUILDSTDERR: 163493 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:13098:0: BUILDSTDERR: 13098 | DO 40 I = ILO, IHI - 1 - NX, NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:5405:0: BUILDSTDERR: 5405 | COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:5405:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:9898:0: BUILDSTDERR: 9898 | $ MAXWRK = MAX( MAXWRK, N+2*SDIM*( N-SDIM ) ) BUILDSTDERR: | BUILDSTDERR: Warning: 'maxwrk' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:16972:0: BUILDSTDERR: 16972 | IF( M.GE.MNTHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:18898:0: BUILDSTDERR: 18898 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:25273:0: BUILDSTDERR: 25273 | IF( LWORK.GE.WRKBL+2*LDA*N ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:24782:0: BUILDSTDERR: 24782 | IF( M.GE.MNTHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:25739:0: BUILDSTDERR: 25739 | IF( LWORK.GE.2*N*N+MAX( N+M, 4*N, BDSPAC ) ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'bdspac' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:29680:0: BUILDSTDERR: 29680 | COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:29680:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:55813:0: BUILDSTDERR: 55813 | A( K+NB, NB ) = EI BUILDSTDERR: | BUILDSTDERR: Warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:60141:0: BUILDSTDERR: 60141 | DOUBLE PRECISION SCALE, S, VALUE, AA, TEMP BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97738:0: BUILDSTDERR: 97738 | $ WORK(IORBDB), LORBDBWORK, CHILDINFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'itauq2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97738:0: Warning: 'itauq1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97738:0: Warning: 'itaup2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97738:0: Warning: 'itaup1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97795:0: BUILDSTDERR: 97795 | $ WORK(IORGQR), LORGQRWORK, INFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'iorgqr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97772:0: BUILDSTDERR: 97772 | $ WORK(IORGLQ), LORGLQWORK, INFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'iorglq' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97738:0: BUILDSTDERR: 97738 | $ WORK(IORBDB), LORBDBWORK, CHILDINFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'iorbdb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: BUILDSTDERR: 97812 | $ WORK(IB22E), WORK(IBBCSD), LBBCSDWORK, INFO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ibbcsd' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib22e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib22d' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib21e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib21d' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib12e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib12d' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib11e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:97812:0: Warning: 'ib11d' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:100327:0: BUILDSTDERR: 100327 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:106741:0: BUILDSTDERR: 106741 | SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:106741:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:110628:0: BUILDSTDERR: 110628 | SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:110628:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:113309:0: BUILDSTDERR: 113309 | SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: dlapack.f:113309:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:1780:19: BUILDSTDERR: 1780 | K = SCALE( I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:1794:19: BUILDSTDERR: 1794 | K = SCALE( I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:2456:21: BUILDSTDERR: 2456 | D( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:2475:24: BUILDSTDERR: 2475 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:2500:21: BUILDSTDERR: 2500 | D( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:2519:24: BUILDSTDERR: 2519 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:21690:21: BUILDSTDERR: 21690 | D( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:21730:24: BUILDSTDERR: 21730 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:21774:21: BUILDSTDERR: 21774 | D( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:21808:24: BUILDSTDERR: 21808 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:3759:21: BUILDSTDERR: 3759 | HSWORK = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:50903:18: BUILDSTDERR: 50903 | LWKOPT = WORK( 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:18862:18: BUILDSTDERR: 18862 | W( 1 ) = A( 1, 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:38115:26: BUILDSTDERR: 38115 | E( I-1 ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:38169:24: BUILDSTDERR: 38169 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19996:24: BUILDSTDERR: 19996 | D( J ) = A( J, J ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19582:21: BUILDSTDERR: 19582 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19610:23: BUILDSTDERR: 19610 | D( I+1 ) = A( I+1, I+1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19613:18: BUILDSTDERR: 19613 | D( 1 ) = A( 1, 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19626:21: BUILDSTDERR: 19626 | E( I ) = ALPHA BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19655:21: BUILDSTDERR: 19655 | D( I ) = A( I, I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19658:18: BUILDSTDERR: 19658 | D( N ) = A( N, N ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:20028:24: BUILDSTDERR: 20028 | D( J ) = A( J, J ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:19253:18: BUILDSTDERR: 19253 | W( 1 ) = A( 1, 1 ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:39333:18: BUILDSTDERR: 39333 | AII = A( I, I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:39352:18: BUILDSTDERR: 39352 | AII = A( I, I ) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:39774:18: BUILDSTDERR: 39774 | AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( 1, J ), 1, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:39801:18: BUILDSTDERR: 39801 | AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( J, 1 ), LDA, BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1) [-Wconversion] BUILDSTDERR: cmplx.f:42206:0: BUILDSTDERR: 42206 | INTEGER I, INFO, IX, J, JX, KX BUILDSTDERR: | BUILDSTDERR: Warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:42834:0: BUILDSTDERR: 42834 | $ CALL ZSWAP( N-KP, A( KP+1, KK ), 1, A( KP+1, KP ), 1 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:23865:0: BUILDSTDERR: 23865 | INTEGER I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2 BUILDSTDERR: | BUILDSTDERR: Warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:28016:0: BUILDSTDERR: 28016 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:27532:0: BUILDSTDERR: 27532 | DOUBLE PRECISION ABSA, SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:44370:0: BUILDSTDERR: 44370 | IF( ILBACK ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:44246:0: BUILDSTDERR: 44246 | IF( ILALL ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilall' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:27310:0: BUILDSTDERR: 27310 | DOUBLE PRECISION SCALE, SUM, VALUE, TEMP BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:15026:0: BUILDSTDERR: 15026 | A( N, N ) = DCMPLX( SMIN, ZERO ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:15008:0: BUILDSTDERR: 15008 | $ CALL ZSWAP( N, A( 1, JPV ), 1, A( 1, I ), 1 ) BUILDSTDERR: | BUILDSTDERR: Warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:15002:0: BUILDSTDERR: 15002 | $ CALL ZSWAP( N, A( IPV, 1 ), LDA, A( I, 1 ), LDA ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:27775:0: BUILDSTDERR: 27775 | DOUBLE PRECISION SCALE, SUM, VALUE BUILDSTDERR: | BUILDSTDERR: Warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:20898:0: BUILDSTDERR: 20898 | IF( ILZ ) BUILDSTDERR: | BUILDSTDERR: Warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:20840:0: BUILDSTDERR: 20840 | IF( ILQ ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:20732:0: BUILDSTDERR: 20732 | IF( .NOT.ILSCHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:25696:0: BUILDSTDERR: 25696 | $ DIFRJ ) / ( POLES( I, 2 )+DJ ) BUILDSTDERR: | BUILDSTDERR: Warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:24636:0: BUILDSTDERR: 24636 | $ CALL ZSCAL( I2-I, DCONJG( TEMP ), H( I, I+1 ), LDH ) BUILDSTDERR: | BUILDSTDERR: Warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:24973:0: BUILDSTDERR: 24973 | A( K+NB, NB ) = EI BUILDSTDERR: | BUILDSTDERR: Warning: 'IMAGPART_EXPR ' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:24973:0: Warning: 'REALPART_EXPR ' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:46945:0: BUILDSTDERR: 46945 | SCALE = SCALE2 BUILDSTDERR: | BUILDSTDERR: Warning: 'scale2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:49028:0: BUILDSTDERR: 49028 | WORK( 1 ) = LWMIN BUILDSTDERR: | BUILDSTDERR: Warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:55232:0: BUILDSTDERR: 55232 | IF( LWORK.LT.NW*NB+TSIZE ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:51959:0: BUILDSTDERR: 51959 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:4925:0: BUILDSTDERR: 4925 | DO 40 I = ILO, IHI - 1 - NX, NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:6411:0: BUILDSTDERR: 6411 | IF( M.GE.MNTHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:11687:0: BUILDSTDERR: 11687 | IF( LWORK.GE.WRKBL+2*LDA*N ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:11158:0: BUILDSTDERR: 11158 | IF( M.GE.MNTHR ) THEN BUILDSTDERR: | BUILDSTDERR: Warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:14657:0: BUILDSTDERR: 14657 | COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) BUILDSTDERR: | BUILDSTDERR: Warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:14657:0: Warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: cmplx.f:52750:0: BUILDSTDERR: 52750 | IWS = LDWORK*NB BUILDSTDERR: | BUILDSTDERR: Warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized] trong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c sock.c -o sock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' mkdir -p -- /builddir/build/BUILD/R-3.6.0/modules make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' making Lapack.d from Lapack.c make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dlamch.f -o dlamch.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dlapack.f -o dlapack.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c cmplx.f -o cmplx.o gcc -shared -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libRlapack.so dlamch.o dlapack.o cmplx.o -L"../../../lib" -lRblas -L -L -lgfortran -lm make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Lapack.c -o Lapack.o gcc -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lapack.so Lapack.o -lR -L"../../../lib" -lRlapack -L"../../../lib" -lRblas -L -L -lgfortran -lm make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' /builddir/build/BUILD/R-3.6.0/lib/libRlapack.so is unchanged make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devX11.c -o devX11.o gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rotated.c -o rotated.o gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbitmap.c -o rbitmap.o gcc -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dataentry.c -o dataentry.o gcc -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' mkdir -p -- ../../library make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/profile' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/translations' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/translations' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/translations' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/base' building package 'base' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/base' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/base' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c text.c -o text.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rmd5.c -o Rmd5.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c md5.c -o md5.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c signals.c -o signals.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c install.c -o install.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c getfmts.c -o getfmts.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c http.c -o http.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gramLatex.c -o gramLatex.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gramRd.c -o gramRd.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/compiler' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/base' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tools' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c io.c -o io.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c size.c -o size.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sock.c -o sock.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stubs.c -o stubs.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c utils.c -o utils.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/utils' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c axis_scales.c -o axis_scales.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chull.c -o chull.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devices.c -o devices.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stubs.c -o stubs.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c colors.c -o colors.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devCairo.c -o devCairo.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devPicTeX.c -o devPicTeX.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devPS.c -o devPS.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c devQuartz.c -o devQuartz.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[8]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' make[9]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cairoBM.c -o cairoBM.o gcc -shared -L"../../../../../lib" -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' make[8]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' make[7]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src/cairo' make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grDevices' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c base.c -o base.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c graphics.c -o graphics.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c par.c -o par.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plot.c -o plot.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plot3d.c -o plot3d.o gcc -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stem.c -o stem.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/graphics' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c kmeans.c -o kmeans.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ansari.c -o ansari.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bandwidths.c -o bandwidths.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chisqsim.c -o chisqsim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c d2x2xk.c -o d2x2xk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fexact.c -o fexact.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c kendall.c -o kendall.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ks.c -o ks.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c line.c -o line.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c smooth.c -o smooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c prho.c -o prho.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c swilk.c -o swilk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ksmooth.c -o ksmooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c loessc.c -o loessc.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c monoSpl.c -o monoSpl.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c isoreg.c -o isoreg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Srunmed.c -o Srunmed.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dblcen.c -o dblcen.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c distance.c -o distance.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c hclust-utils.c -o hclust-utils.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nls.c -o nls.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rWishart.c -o rWishart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c HoltWinters.c -o HoltWinters.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c PPsum.c -o PPsum.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c arima.c -o arima.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c burg.c -o burg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c filter.c -o filter.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mAR.c -o mAR.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pacf.c -o pacf.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c starma.c -o starma.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c port.c -o port.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c family.c -o family.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sbart.c -o sbart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c approx.c -o approx.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c loglin.c -o loglin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lowess.c -o lowess.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c massdist.c -o massdist.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c splines.c -o splines.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lm.c -o lm.o BUILDSTDERR: gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c complete_cases.c -o cofft.c: In function 'fft_work': BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ BUILDSTDERR: fft.c:148:9: warning: array subscript -1 is outside array bounds of 'int[20]' [-Warray-bounds] BUILDSTDERR: 148 | nfac--;/*the global one!*/ BUILDSTDERR: | ~~~~^~ BUILDSTDERR: fft.c:730:12: note: while referencing 'nfac' BUILDSTDERR: 730 | static int nfac[20]; BUILDSTDERR: | ^~~~ mplete_cases.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cov.c -o cov.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c deriv.c -o deriv.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fft.c -o fft.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fourier.c -o fourier.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c model.c -o model.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c optim.c -o optim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c optimize.c -o optimize.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c integrate.c -o integrate.o BUILDSTDERR: gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_Aloessf.f:59:14: BUILDSTDERR: 59 | j=DBLE(j)/2.D0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:1893:14: BUILDSTDERR: 1893 | m=DBLE(l+u)/2.D0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:1398:20: BUILDSTDERR: 1398 | i=phi(pi(ii)) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:927:12: BUILDSTDERR: 927 | lg=DBLE(lg)/2.D0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:522:22: BUILDSTDERR: 522 | if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:1204:13: BUILDSTDERR: 1204 | ifloor=x BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:834:22: BUILDSTDERR: 834 | if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:1582:18: BUILDSTDERR: 1582 | i1=dble((d+2)*(d+1))/2.d0 BUILDSTDERR: | 1 BUILDSTDERR: Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] BUILDSTDERR: loessf.f:472:25: BUILDSTDERR: 472 | subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:472:39: BUILDSTDERR: 472 | subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:827:31: BUILDSTDERR: 827 | subroutine ehg197(deg,tau,d,f,dk,trl) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1984:31: BUILDSTDERR: 1984 | subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1984:47: BUILDSTDERR: 1984 | subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1984:53: BUILDSTDERR: 1984 | subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1497:50: BUILDSTDERR: 1497 | subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1497:53: BUILDSTDERR: 1497 | subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1648:30: BUILDSTDERR: 1648 | subroutine lowese(iv,liv,lv,wv,m,z,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1648:33: BUILDSTDERR: 1648 | subroutine lowese(iv,liv,lv,wv,m,z,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1667:39: BUILDSTDERR: 1667 | subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1667:42: BUILDSTDERR: 1667 | subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1699:30: BUILDSTDERR: 1699 | subroutine lowesl(iv,liv,lv,wv,m,z,l) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1699:33: BUILDSTDERR: 1699 | subroutine lowesl(iv,liv,lv,wv,m,z,l) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1721:33: BUILDSTDERR: 1721 | subroutine lowesr(yy,iv,liv,lv,wv) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] BUILDSTDERR: loessf.f:1721:36: BUILDSTDERR: 1721 | subroutine lowesr(yy,iv,liv,lv,wv) BUILDSTDERR: | 1 BUILDSTDERR: Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] SSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c random.c -o random.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c distn.c -o distn.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c zeroin.c -o zeroin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rcont.c -o rcont.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c influence.c -o influence.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c loessf.f -o loessf.o BUILDSTDERR: gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c ppr.portsrc.f:6569:0: BUILDSTDERR: 6569 | INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC, BUILDSTDERR: | BUILDSTDERR: Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:5516:0: BUILDSTDERR: 5516 | IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) BUILDSTDERR: | BUILDSTDERR: Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:5653:0: BUILDSTDERR: 5653 | IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310 BUILDSTDERR: | BUILDSTDERR: Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:10324:0: BUILDSTDERR: 10324 | IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) BUILDSTDERR: | BUILDSTDERR: Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:10407:0: BUILDSTDERR: 10407 | V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA) BUILDSTDERR: | BUILDSTDERR: Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:10319:0: BUILDSTDERR: 10319 | LK = DMAX1(LK, PHI*W(PHIPIN)) BUILDSTDERR: | BUILDSTDERR: Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:10461:0: BUILDSTDERR: 10461 | IF (KA .GE. KAMIN) GO TO 340 BUILDSTDERR: | BUILDSTDERR: Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:12238:0: BUILDSTDERR: 12238 | V(NREDUC) = NRED BUILDSTDERR: | BUILDSTDERR: Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:12241:0: BUILDSTDERR: 12241 | V(DST0) = DNWTST BUILDSTDERR: | BUILDSTDERR: Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:2510:0: BUILDSTDERR: 2510 | V(NREDUC) = NRED BUILDSTDERR: | BUILDSTDERR: Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:2509:0: BUILDSTDERR: 2509 | 60 V(DST0) = DS0 BUILDSTDERR: | BUILDSTDERR: Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:8169:0: BUILDSTDERR: 8169 | V(NREDUC) = NRED BUILDSTDERR: | BUILDSTDERR: Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:8168:0: BUILDSTDERR: 8168 | 90 V(DST0) = DS0 BUILDSTDERR: | BUILDSTDERR: Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:8647:0: BUILDSTDERR: 8647 | 210 IV(FDH) = HES BUILDSTDERR: | BUILDSTDERR: Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:3582:0: BUILDSTDERR: 3582 | IF (LIV .LT. MIV2) GO TO 300 BUILDSTDERR: | BUILDSTDERR: Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:12074:0: BUILDSTDERR: 12074 | 270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) BUILDSTDERR: | BUILDSTDERR: Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:453:0: BUILDSTDERR: 453 | 300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) BUILDSTDERR: | BUILDSTDERR: Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:361:0: BUILDSTDERR: 361 | CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1)) BUILDSTDERR: | BUILDSTDERR: Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: portsrc.f:361:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized] f -o ppr.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c stl.f -o stl.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c lminfl.f -o lminfl.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -L -L -lgfortran -lm -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/datasets' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/datasets' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c making utils.d from utils.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c do_substitute_direct.c -o do_substitute_direct.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c slot.c -o slot.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c class_support.c -o class_support.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c tests.c -o tests.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c utils.c -o utils.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/methods' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gpar.c -o gpar.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c grid.c -o grid.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c just.c -o just.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c layout.c -o layout.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c matrix.c -o matrix.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c register.c -o register.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c state.c -o state.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c unit.c -o unit.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c util.c -o util.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c viewport.c -o viewport.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/grid' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines/src' making splines.d from splines.c gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c splines.c -o splines.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o splines.so splines.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/splines' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/stats4' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c tcltk.c -o tcltk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c tcltk_unix.c -o tcltk_unix.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 -L/usr/lib64 -ltk8.6 -lX11 -lm -L../../../../lib -lR make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk/src' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/tcltk' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' make[5]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rngstream.c -o rngstream.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fork.c -o fork.o gcc -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[6]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel/src' make[5]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel/src' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' make[4]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/parallel' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/base' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/tests' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/tests' you should 'make docs' now ... make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc' creating doc/NEWS creating doc/NEWS.pdf make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-data.html creating doc/manual/R-exts.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/html' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/html' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' installing parsed Rd make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' building/updating package metadata ... make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' writing package indices make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' building all R object docs converting help for package 'base' Arithmetic html Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/Arithmetic.Rd:158: file link 'Ops' in package 'base' does not exist and so has been treated as a topic AsIs html Bessel html CallExternal html Colon html Comparison html Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/Comparison.Rd:101: file link 'Ops' in package 'base' does not exist and so has been treated as a topic Constants html Control html Cstack_info html DateTimeClasses html Dates html Defunct html Deprecated html Encoding html EnvVar html Extract html Extract.data.frame html 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html getCallingDLL html getDLLRegisteredRoutines html getLoadedDLLs html getNativeSymbolInfo html gettext html getwd html gl html grep html grepRaw html groupGeneric html grouping html gzcon html hexmode html iconv html icuSetCollate html identical html identity html ifelse html integer html interaction html interactive html invisible html is.finite html is.function html is.language html is.object html is.recursive html is.single html is.unsorted html isR html isS4 html isSymmetric html jitter html kappa html kronecker html l10n_info html labels html lapply html lazyload html length html lengths html levels html libPaths html libcurlVersion html library html library.dynam html license html list html list.files html list2env html load html locales html logical html lower.tri html ls html make.names html make.unique html mapply html margin.table html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memlimits html memory.profile html merge html message html missing html mode html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pcre_config html pmatch html polyroot html pos.to.env html pretty html print html Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/base/man/print.Rd:86: file link '.print.via.format' in package 'tools' does not exist and so has been treated as a topic print.dataframe html print.default html prmatrix html proc.time html prod html prop.table html pushBack html qr html qraux html quit html range html rank html rapply html raw html rawConnection html rawConversion html readBin html readChar html readLines html readRDS html readRenviron html readline html reg.finalizer html regex html regmatches html rep html replace html rev html rle html rm html round.POSIXt html row html row.names html rowsum html sQuote html sample html save html scale html scan html search html seek html seq.Date html seq.POSIXt html seq html sequence html serialize html setTimeLimit html sets html shQuote html showConnections html sign html sink html slice.index html slotOp html socketSelect html solve html sort html source html split html sprintf html srcfile html standardGeneric html startsWith html stop html stopifnot html strptime html strrep html strsplit html strtoi html strtrim html structure html strwrap html subset html substitute html substr html sum html summary html svd html sweep html switch html sys.parent html sys.source html system html system.file html system.time html system2 html t html table html tabulate html tapply html taskCallback html taskCallbackManager html taskCallbackNames html tempfile html textconnections html tilde html timezones html toString html trace html traceback html tracemem html transform html trimws html try html typeof html unique html unlink html unlist html unname html userhooks html utf8Conversion html validUTF8 html vector html warning html warnings html weekday.POSIXt html which html which.min html with html withVisible html write html writeLines html xtfrm html zMachine html zScript html zapsmall html zpackages html zutils html Signals html converting help for package 'tools' CRANtools html HTMLheader html HTMLlinks html QC html Rcmd html Rd2HTML html Rd2txt_options html RdTextFilter html Rdiff html Rdindex html Rdutils html SweaveTeXFilter html add_datalist html assertCondition html bibstyle html buildVignette html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html Rd warning: /builddir/build/BUILD/R-3.6.0/src/library/tools/man/check_packages_in_dir.Rd:123: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html find_gs_cmd html getVignetteInfo html loadRdMacros html makeLazyLoading html make_translations_pkg html makevars html md5sum html package_dependencies html package_native_routine_registration_skeleton html parseLatex html parse_Rd html print.via.format html pskill html psnice html read.00Index html showNonASCII html startDynamicHelp html testInstalledPackage html texi2dvi html toHTML html toRd html toTitleCase html tools-defunct html tools-deprecated html tools-package html undoc html updatePACKAGES html update_pkg_po html vignetteEngine html vignetteInfo html writePACKAGES html xgettext html converting help for package 'utils' BATCH html COMPILE html DLL.version html INSTALL html LINK html PkgUtils html Question html REMOVE html RHOME html RShowDoc html RSiteSearch html Rconsole html Rprof html Rprofmem html Rscript html Rtangle html RweaveLatex html SHLIB html Sweave html SweaveSyntConv html SweaveUtils html URLencode html View html adist html alarm html apropos html aregexec html arrangeWindows html askYesNo html aspell-utils html aspell html available.packages html bibentry html browseEnv html browseURL html browseVignettes html bug.report html capture.output html changedFiles html choose.dir html choose.files html chooseBioCmirror html chooseCRANmirror html citEntry html citation html cite html clipboard html close.socket html combn html compareVersion html contrib.url html count.fields html create.post html data html dataentry html debugcall html debugger html demo html download.file html download.packages html edit html edit.data.frame html example html file.edit html filetest html findLineNum html fix html flush.console html format html getAnywhere html getFromNamespace html getParseData html getS3method html getWindowsHandle html getWindowsHandles html glob2rx html globalVariables html hasName html head html help html help.request html help.search html help.start html hsearch-utils html install.packages html installed.packages html isS3method html isS3stdGen html localeToCharset html ls_str html maintainer html make.packages.html html make.socket html memory.size html menu html methods html mirrorAdmin html modifyList html news html nsl html object.size html package.skeleton html packageDescription html packageName html packageStatus html page html person html process.events html prompt html promptData html promptPackage html rcompgen html read.DIF html read.fortran html read.fwf html read.socket html read.table html readRegistry html recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories html setWindowTitle html shortPathName html sourceutils html stack html str html strcapture html summaryRprof html tar html toLatex html txtProgressBar html type.convert html untar html unzip html update.packages html url.show html utils-defunct html utils-deprecated html utils-package html vignette html warnErrList html winDialog html winMenus html winProgressBar html winextras html write.table html zip html converting help for package 'grDevices' Devices html Hershey html Japanese html Type1Font html adjustcolor html as.graphicsAnnot html as.raster html axisTicks html boxplot.stats html bringToTop html cairo html check.options html chull html cm html col2rgb html colorRamp html colors html contourLines html convertColor html densCols html dev html dev.capabilities html dev.capture html dev.flush html dev.interactive html dev.size html dev2 html dev2bitmap html devAskNewPage html embedFonts html extendrange html getGraphicsEvent html grDevices-package html grSoftVersion html gray html gray.colors html hcl html hsv html make.rgb html msgWindow html n2mfrow html nclass html palette html palettes html pdf html pdf.options html pictex html plotmath html postscript html postscriptFonts html pretty.Date html ps.options html quartz html quartzFonts html recordGraphics html recordplot html rgb html rgb2hsv html trans3d html windows html windows.options html windowsFonts html x11 html x11Fonts html xfig html xy.coords html xyTable html xyz.coords html png html savePlot html converting help for package 'graphics' abline html arrows html assocplot html axTicks html axis.POSIXct html axis html barplot html box html boxplot html boxplot.matrix html bxp html cdplot html clip html contour html convertXY html coplot html curve html dotchart html filled.contour html fourfoldplot html frame html graphics-defunct html graphics-package html grid html hist.POSIXt html hist html identify html image html layout html legend html lines html locator html matplot html mosaicplot html mtext html pairs html panel.smooth html par html persp html pie html plot html plot.dataframe html plot.default html plot.design html plot.factor html plot.formula html plot.raster html plot.table html plot.window html plot.xy html plothistogram html points html polygon html polypath html rasterImage html rect html rug html screen html segments html smoothScatter html spineplot html stars html stem html stripchart html strwidth html sunflowerplot html symbols html text html title html units html xspline html zAxis html converting help for package 'stats' AIC html ARMAacf html ARMAtoMA html Beta html Binomial html Cauchy html Chisquare html Distributions html Exponential html Fdist html GammaDist html Geometric html HoltWinters html Hypergeometric html IQR html KalmanLike html Logistic html Lognormal html Multinom html NLSstAsymptotic html NLSstClosestX html NLSstLfAsymptote html NLSstRtAsymptote html NegBinomial html Normal html Poisson html SSD html SSasymp html SSasympOff html SSasympOrig html SSbiexp html SSfol html SSfpl html SSgompertz html SSlogis html SSmicmen html SSweibull html SignRank html StructTS html TDist html Tukey html TukeyHSD html Uniform html Weibull html Wilcoxon html acf html acf2AR html add1 html addmargins html aggregate html alias html anova html anova.glm html anova.lm html anova.mlm html ansari.test html aov html approxfun html ar html ar.ols html arima html arima.sim html arima0 html as.hclust html asOneSidedFormula html ave html bandwidth html bartlett.test html binom.test html biplot html biplot.princomp html birthday html box.test html cancor html case.names html checkMFClasses html chisq.test html cmdscale html coef html complete.cases html confint html constrOptim html contrast html contrasts html convolve html cophenetic html cor html cor.test html cov.wt html cpgram html cutree html decompose html delete.response html dendrapply html dendrogram html density html deriv html deviance html df.residual html diffinv html dist html dummy.coef html ecdf html eff.aovlist html effects html embed html expand.model.frame html extractAIC html factanal html factor.scope html family html fft html filter html fisher.test html fitted.values html fivenum html fligner.test html formula html formula.nls html friedman.test html ftable html ftable.formula html getInitial html glm html glm.control html glm.summaries html hclust html heatmap html identify.hclust html influence.measures html integrate html interaction.plot html is.empty html isoreg html kernapply html kernel html kmeans html kruskal.test html ks.test html ksmooth html lag html lag.plot html line html listof html lm html lm.influence html lm.summaries html lmfit html loadings html loess html loess.control html logLik html loglin html lowess html ls.diag html ls.print html lsfit html mad html mahalanobis html make.link html makepredictcall html manova html mantelhaen.test html mauchly.test html mcnemar.test html median html medpolish html model.extract html model.frame html model.matrix html model.tables html monthplot html mood.test html na.action html na.contiguous html na.fail html nafns html naprint html nextn html nlm html nlminb html nls html nls.control html nobs html numericDeriv html offset html oneway.test html optim html optimize html order.dendrogram html p.adjust html pairwise.prop.test html pairwise.t.test html pairwise.table html pairwise.wilcox.test html plot.HoltWinters html plot.acf html plot.density html plot.isoreg html plot.lm html plot.ppr html plot.profile.nls html plot.spec html plot.stepfun html plot.ts html poisson.test html poly html power html power.anova.test html power.prop.test html power.t.test html pp.test html ppoints html ppr html prcomp html predict.HoltWinters html predict html predict.arima html predict.glm html predict.lm html predict.loess html predict.nls html predict.smooth.spline html preplot html princomp html print.power.htest html print.ts html printCoefmat html profile html profile.nls html proj html prop.test html prop.trend.test html qqnorm html quade.test html quantile html r2dtable html rWishart html read.ftable html rect.hclust html relevel html reorder.dendrogram html reorder.factor html replications html reshape html residuals html runmed html scatter.smooth html screeplot html sd html se.contrast html selfStart html setNames html shapiro.test html sigma html simulate html smooth html smooth.spline html smoothEnds html sortedXyData html spec.ar html spec.pgram html spec.taper html spectrum html splinefun html start html stat.anova html stats-defunct html stats-deprecated html stats-package html step html stepfun html stl html stlmethods html summary.aov html summary.glm html summary.lm html summary.manova html summary.nls html summary.princomp html supsmu html symnum html t.test html termplot html terms html terms.formula html terms.object html time html toeplitz html ts-methods html ts html ts.plot html ts.union html tsSmooth html tsdiag html tsp html uniroot html update html update.formula html var.test html varimax html vcov html weighted.mean html weighted.residuals html weights html wilcox.test html window html xtabs html zC html converting help for package 'datasets' AirPassengers html BJsales html BOD html ChickWeight html DNase html EuStockMarkets html Formaldehyde html HairEyeColor html Harman23.cor html Harman74.cor html Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html npk html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Classes_Details html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html Introduction html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html Methods_Details html Methods_for_Nongenerics html Methods_for_S3 html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html removeMethod html representation html selectSuperClasses html setAs html setClass html setClassUnion html setGeneric html setGroupGeneric html setIs html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html calcStringMetric html current.viewport html dataViewport html depth html deviceLoc html drawDetails html editDetails html explode html gEdit html gPath html getNames html gpar html grid-defunct html grid-internal html grid-package html grid.DLapply html grid.add html grid.bezier html grid.cap html grid.circle html grid.clip html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grep html grid.grill html grid.grob html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobCoords html grobName html grobWidth html grobX html legendGrob html makeContent html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html valid.just html validDetails html viewport html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/Recommended' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library/Recommended' begin installing recommended package MASS * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpkLXND2/R.INSTALL62b71c734c2b/MASS/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c MASS.c -o MASS.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lqs.c -o lqs.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o MASS.so MASS.o lqs.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpkLXND2/R.INSTALL62b71c734c2b/MASS/src' installing to /builddir/build/BUILD/R-3.6.0/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done begin installing recommended package lattice * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpkEWvVv/R.INSTALL62e46c98b5c/lattice/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c threeDplot.c -o threeDplot.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lattice.so init.o threeDplot.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpkEWvVv/R.INSTALL62e46c98b5c/lattice/src' installing to /builddir/build/BUILD/R-3.6.0/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' finding HTML links ... done Lattice html Rows html USMortality html axis.default html banking html barchart.table html barley html cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done begin installing recommended package Matrix * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c CHMfactor.c -o CHMfactor.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Csparse.c -o Csparse.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c TMatrix_as.c -o TMatrix_as.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Tsparse.c -o Tsparse.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Mutils.c -o Mutils.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chm_common.c -o chm_common.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 1408 | csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai, | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cs_utils.c -o cs_utils.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dense.c -o dense.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgCMatrix.c -o dgCMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgTMatrix.c -o dgTMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgeMatrix.c -o dgeMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dpoMatrix.c -o dpoMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dppMatrix.c -o dppMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dsCMatrix.c -o dsCMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dsyMatrix.c -o dsyMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dspMatrix.c -o dspMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dtCMatrix.c -o dtCMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dtTMatrix.c -o dtTMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dtrMatrix.c -o dtrMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dtpMatrix.c -o dtpMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c factorizations.c -o factorizations.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ldense.c -o ldense.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgCMatrix.c -o lgCMatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sparseQR.c -o sparseQR.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c abIndex.c -o abIndex.o make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD' ( cd Lib ; make clean ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD/Lib' make[5]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD' ( cd Source ; make clean ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD/Source' make[5]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD' ( cd Source ; make clean ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD/Source' make[5]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/SuiteSparse_config' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD' ( cd Lib ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD/Lib' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_aat.c -o cholmod_aat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_add.c -o cholmod_add.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_band.c -o cholmod_band.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o In file included from ../Core/cholmod_change_factor.c:116: ../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] 40 | double *Lx, *Lz ; | ^~ In file included from ../Core/cholmod_change_factor.c:118: ../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] 40 | 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] 265 | 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] 680 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] 680 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 679 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] 679 | 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] 827 | 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] 826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~~ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] 826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_common.c -o cholmod_common.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_complex.c -o cholmod_complex.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 278 | 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] 278 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_dense.c -o cholmod_dense.o In file included from ../Core/cholmod_dense.c:48: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ In file included from ../Core/cholmod_dense.c:50: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | 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] 136 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 136 | 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] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ In file included from ../Core/cholmod_dense.c:52: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | 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] 136 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 136 | 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] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 229 | 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] 303 | Int i, n, nz ; | ^~ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 302 | double *Xx, *Xz ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_error.c -o cholmod_error.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_factor.c -o cholmod_factor.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_memory.c -o cholmod_memory.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 488 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ; | ^~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_transpose.c -o cholmod_transpose.o In file included from ../Core/cholmod_transpose.c:124: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:126: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:128: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:131: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:133: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ In file included from ../Core/cholmod_transpose.c:136: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_triplet.c -o cholmod_triplet.o In file included from ../Core/cholmod_triplet.c:108: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:110: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:112: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | 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] 345 | 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] 344 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Core/cholmod_version.c -o cholmod_version.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 207 | 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] 961 | 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] 1508 | 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] 1506 | 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] 1505 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, | ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] 1507 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, | ^~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Check/cholmod_read.c -o cholmod_read.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 365 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, | ^~~~~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 422 | 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] 419 | 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] 419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 114 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:164: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:166: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:168: ../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] 51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:172: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:174: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:176: ../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] 51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o In file included from ../Cholesky/cholmod_solve.c:66: ../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] 64 | double *Lx, *Yx, *Yz ; | ^~ In file included from ../Cholesky/cholmod_solve.c:69: ../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] 64 | 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] 337 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:46: ../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] 55 | 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] 52 | 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] 52 | 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] 52 | 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] 52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../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] 55 | 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] 52 | 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] 52 | 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] 52 | 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] 52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:50: ../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] 55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 410 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; | ^~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:78: ../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] 111 | 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] 111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:80: ../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] 111 | 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] 111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28: ../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] 33 | 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] 241 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ In file included from ../Supernodal/cholmod_super_solve.c:30: ../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] 33 | 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] 241 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 455 | Int totsize ; | ^~~~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o In file included from ../Core/cholmod_change_factor.c:116: ../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] 40 | double *Lx, *Lz ; | ^~ In file included from ../Core/cholmod_change_factor.c:118: ../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] 40 | 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] 265 | 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] 680 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] 680 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 679 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] 679 | 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] 827 | 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] 826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~~ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] 826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 278 | 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] 278 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o In file included from ../Core/cholmod_dense.c:48: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ In file included from ../Core/cholmod_dense.c:50: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | 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] 136 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 136 | 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] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ In file included from ../Core/cholmod_dense.c:52: ../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] 30 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 30 | 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] 136 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 136 | 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] 229 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 229 | 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] 303 | Int i, n, nz ; | ^~ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 302 | double *Xx, *Xz ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 488 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ; | ^~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o In file included from ../Core/cholmod_transpose.c:124: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:126: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:128: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:131: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 45 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 45 | 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] 143 | 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] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 142 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:133: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ In file included from ../Core/cholmod_transpose.c:136: ../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] 47 | 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] 47 | 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] 47 | 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] 46 | 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] 46 | 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] 143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o In file included from ../Core/cholmod_triplet.c:108: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:110: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:112: ../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] 31 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 31 | 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] 345 | 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] 344 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 207 | 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] 961 | 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] 1508 | 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] 1506 | 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] 1505 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, | ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] 1507 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, | ^~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 365 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, | ^~~~~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 422 | 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] 419 | 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] 419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 114 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:164: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:166: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:168: ../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] 51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:172: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:174: ../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] 51 | 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] 47 | 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] 47 | 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] 47 | 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] 47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:176: ../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] 51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o In file included from ../Cholesky/cholmod_solve.c:66: ../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] 64 | double *Lx, *Yx, *Yz ; | ^~ In file included from ../Cholesky/cholmod_solve.c:69: ../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] 64 | 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] 337 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:46: ../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] 55 | 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] 52 | 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] 52 | 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] 52 | 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] 52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../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] 55 | 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] 52 | 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] 52 | 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] 52 | 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] 52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:50: ../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] 55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 410 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; | ^~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:78: ../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] 111 | 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] 111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:80: ../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] 111 | 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] 111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28: ../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] 33 | 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] 241 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ In file included from ../Supernodal/cholmod_super_solve.c:30: ../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] 33 | 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] 241 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 455 | 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/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD' ( cd Source ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD/Source' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c colamd_global.c -o colamd_global.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c colamd.c -o colamd.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD' ( cd Source ; make -f "/builddir/build/BUILD/R-3.6.0/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD/Source' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_1.c -o amd_i_1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_1.c -o amd_l_1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_2.c -o amd_i_2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_2.c -o amd_l_2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_order.c -o amd_i_order.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_order.c -o amd_l_order.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_control.c -o amd_i_control.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_control.c -o amd_l_control.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_info.c -o amd_i_info.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_info.c -o amd_l_info.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I../Include -DDINT -c amd_global.c -o amd_i_global.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/AMD' make[4]: Entering directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/SuiteSparse_config' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src/SuiteSparse_config' gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/builddir/build/BUILD/R-3.6.0/lib -lRlapack -L/builddir/build/BUILD/R-3.6.0/lib -lRblas -L -L -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/src' installing to /builddir/build/BUILD/R-3.6.0/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html KhatriRao html LU-class html Matrix-class html Matrix html MatrixClass html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html Rd warning: /tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic abIseq html all-methods html all.equal-methods html atomicVector-class html band html bandSparse html bdiag html boolean-matprod html cBind html chol html chol2inv-methods html colSums html compMatrix-class html condest html dMatrix-class html ddenseMatrix-class html ddiMatrix-class html denseMatrix-class html dgCMatrix-class html dgRMatrix-class html dgTMatrix-class html dgeMatrix-class html diagU2N html diagonalMatrix-class html dpoMatrix-class html drop0 html dsCMatrix-class html dsRMatrix-class html dsparseMatrix-class html dsyMatrix-class html dtCMatrix-class html dtRMatrix-class-def html dtpMatrix-class html dtrMatrix-class html expand html expm html externalFormats html facmul html forceSymmetric html formatSparseM html generalMatrix-class html graph2T html image-methods html Rd warning: /tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/man/image-methods.Rd:81: file link 'get.gpar' in package 'grid' does not exist and so has been treated as a topic indMatrix-class html index-class html invPerm html is.na-methods html is.null.DN html isSymmetric-methods html isTriangular html kronecker-methods html ldenseMatrix-class html ldiMatrix-class html lgeMatrix-class html lsparseMatrix-classes html lsyMatrix-class html ltrMatrix-class html lu html matrix-products html Rd warning: /tmp/RtmpbMsdN7/R.INSTALL6321d0174f3/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic nMatrix-class html ndenseMatrix-class html nearPD html ngeMatrix-class html nnzero html norm html nsparseMatrix-classes html nsyMatrix-class html ntrMatrix-class html number-class html pMatrix-class html printSpMatrix html qr-methods html rankMatrix html rcond html rep2abI html replValue-class html rleDiff-class html rsparsematrix html solve-methods html spMatrix html sparse.model.matrix html sparseLU-class html sparseMatrix-class html sparseMatrix html sparseQR-class html sparseVector-class html sparseVector html symmetricMatrix-class html symmpart html triangularMatrix-class html uniqTsparse html unpack html unused-classes html updown html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done begin installing recommended package nlme * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/src' gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c chol.f -o chol.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c corStruct.c -o corStruct.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gnls.c -o gnls.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c matrix.c -o matrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nlOptimizer.c -o nlOptimizer.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nlme.c -o nlme.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nlmefit.c -o nlmefit.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pdMat.c -o pdMat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pythag.c -o pythag.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c rs.f -o rs.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L -L -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/src' installing to /builddir/build/BUILD/R-3.6.0/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls-internal html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html Rd warning: /tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html Rd warning: /tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpVWYjmM/R.INSTALL65a524dfe3c6/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html varExp html varFixed html varFunc html varIdent html varPower html varWeights html varWeights.glsStruct html varWeights.lmeStruct html ** building package indices ** testing if installed package can be loaded * DONE (nlme) Making 'packages.html' ... done begin installing recommended package survival * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/Rtmp0IonxH/R.INSTALL66006cfb0d79/survival/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agexact.c -o agexact.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agfit4.c -o agfit4.o agfit4.c: In function 'agfit4': agfit4.c:593:29: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized] 593 | else if (start[p] < dtime) { | ^ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agfit5.c -o agfit5.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agmart.c -o agmart.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agmart2.c -o agmart2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agmart3.c -o agmart3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agscore.c -o agscore.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agsurv3.c -o agsurv3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agsurv4.c -o agsurv4.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c agsurv5.c -o agsurv5.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chinv2.c -o chinv2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chinv3.c -o chinv3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cholesky2.c -o cholesky2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cholesky3.c -o cholesky3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cholesky5.c -o cholesky5.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chsolve2.c -o chsolve2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chsolve3.c -o chsolve3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chsolve5.c -o chsolve5.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c concordance1.c -o concordance1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c concordance3.c -o concordance3.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cox_Rcallback.c -o cox_Rcallback.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxcount1.c -o coxcount1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxdetail.c -o coxdetail.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxexact.c -o coxexact.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxfit5.c -o coxfit5.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxfit6.c -o coxfit6.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxmart.c -o coxmart.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxmart2.c -o coxmart2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxph_wtest.c -o coxph_wtest.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxsafe.c -o coxsafe.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxscho.c -o coxscho.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxscore.c -o coxscore.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dmatrix.c -o dmatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c doloop.c -o doloop.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c finegray.c -o finegray.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gchol.c -o gchol.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c norisk.c -o norisk.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pyears1.c -o pyears1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pyears2.c -o pyears2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pyears3b.c -o pyears3b.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pystep.c -o pystep.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survConcordance.c -o survConcordance.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survdiff2.c -o survdiff2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survfit4.c -o survfit4.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survfitci.c -o survfitci.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survfitkm.c -o survfitkm.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survpenal.c -o survpenal.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survreg6.c -o survreg6.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survreg7.c -o survreg7.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survregc1.c -o survregc1.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survregc2.c -o survregc2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c survsplit.c -o survsplit.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c tmerge.c -o tmerge.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/Rtmp0IonxH/R.INSTALL66006cfb0d79/survival/src' installing to /builddir/build/BUILD/R-3.6.0/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'survival' finding HTML links ... done Surv html Survmethods html aareg html aeqSurv html agreg.fit html aml html anova.coxph html attrassign html basehaz html bladder html cch html cgd html cgd0 html cipoisson html Rd warning: /tmp/Rtmp0IonxH/R.INSTALL66006cfb0d79/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp0IonxH/R.INSTALL66006cfb0d79/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic clogit html cluster html colon html concordance html concordancefit html cox.zph html coxph html coxph.control html coxph.detail html coxph.object html coxph.wtest html diabetic html dsurvreg html finegray html flchain html frailty html heart html is.ratetable html kidney html levels.Surv html lines.survfit html logLik.coxph html logan html lung html mgus html mgus2 html model.frame.coxph html model.matrix.coxph html myeloid html neardate html nwtco html ovarian html pbc html pbcseq html plot.aareg html plot.cox.zph html plot.survfit html predict.coxph html predict.survreg html print.aareg html print.summary.coxph html print.summary.survexp html print.summary.survfit html print.survfit html pspline html pyears html quantile.survfit html ratetable html ratetableDate html rats html rats2 html reliability html residuals.coxph html residuals.survreg html retinopathy html rhDNase html ridge html solder html stanford2 html statefig html strata html summary.aareg html summary.coxph html summary.pyears html summary.survexp html summary.survfit html survConcordance-deprecated html survSplit html survdiff html survexp html survexp.fit html survexp.object html survexp.us html survfit html survfit.coxph html survfit.formula html survfit.matrix html survfit.object html survfitcoxph.fit html survival-internal html survobrien html survreg html survreg.control html survreg.distributions html survreg.object html survregDtest html tcut html tmerge html tobin html transplant html udca html untangle.specials html uspop2 html vcov.coxph html veteran html xtfrm.Surv html yates html yates_setup html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) Making 'packages.html' ... done begin installing recommended package boot * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'boot' finding HTML links ... done EEF.profile html Imp.Estimates html abc.ci html acme html aids html aircondit html amis html aml html beaver html bigcity html boot-practicals html boot html boot.array html boot.ci html brambles html breslow html calcium html cane html capability html catsM html cav html cd4 html cd4.nested html censboot html channing html claridge html cloth html co.transfer html coal html control html corr html cum3 html cv.glm html darwin html dogs html downs.bc html ducks html empinf html envelope html exp.tilt html fir html freq.array html frets html glm.diag html glm.diag.plots html gravity html hirose html imp.weights html inv.logit html islay html jack.after.boot html k3.linear html linear.approx html lines.saddle.distn html logit html manaus html melanoma html motor html neuro html nitrofen html nodal html norm.ci html nuclear html paulsen html plot.boot html poisons html polar html print.boot html print.bootci html print.saddle.distn html print.simplex html remission html saddle html saddle.distn html saddle.distn.object html salinity html simplex html simplex.object html smooth.f html sunspot html survival html tau html tilt.boot html tsboot html tuna html urine html var.linear html wool html ** building package indices ** testing if installed package can be loaded * DONE (boot) Making 'packages.html' ... done begin installing recommended package cluster * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c clara.c -o clara.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c daisy.f -o daisy.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dysta.f -o dysta.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fanny.c -o fanny.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mona.c -o mona.o mona.c: In function 'clmona_': mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized] 261 | ner[k] = nelbb; | ~~~~~~~^~~~~~~ mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized] 248 | int lcc, nelbb; | ^~~ mona.c:235:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized] 235 | km = ka + jtel2; | ^~ mona.c:235:6: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized] mona.c:227:18: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | if (x[nel + jma * x_dim1] == 1) { | ~~~~^~~~~~~~ mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized] 211 | jtel = c + d; | ~~~~~^~~~~~~ mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized] 212 | jtelz = a + b; | ~~~~~~^~~~~~~ mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pam.c -o pam.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sildist.c -o sildist.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c spannel.c -o spannel.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c twins.c -o twins.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L -L -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/src' installing to /builddir/build/BUILD/R-3.6.0/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html agnes.object html agriculture html animals html bannerplot html chorSub html clara html clara.object html clusGap html clusplot.default html Rd warning: /tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html Rd warning: /tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic fanny html fanny.object html flower html lower.to.upper.tri.inds html mona html mona.object html pam html pam.object html partition.object html plantTraits html plot.agnes html Rd warning: /tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic plot.diana html plot.mona html plot.partition html pltree html pluton html predict.ellipsoid html print.agnes html print.clara html print.diana html print.dissimilarity html Rd warning: /tmp/RtmpAzWo8a/R.INSTALL670f47abb974/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic print.fanny html print.mona html print.pam html ruspini html silhouette html sizeDiss html summary.agnes html summary.clara html summary.diana html summary.mona html summary.pam html twins.object html volume.ellipsoid html votes.repub html xclara html ** building package indices ** testing if installed package can be loaded * DONE (cluster) Making 'packages.html' ... done begin installing recommended package codetools * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done begin installing recommended package foreign * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/Rtmp5SDmKF/R.INSTALL678038330bf1/foreign/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c R_systat.c -o R_systat.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rdbfread.c -o Rdbfread.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c Rdbfwrite.c -o Rdbfwrite.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c SASxport.c -o SASxport.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c avl.c -o avl.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbfopen.c -o dbfopen.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c file-handle.c -o file-handle.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c format.c -o format.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c minitab.c -o minitab.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pfm-read.c -o pfm-read.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sfm-read.c -o sfm-read.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c spss.c -o spss.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stataread.c -o stataread.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/Rtmp5SDmKF/R.INSTALL678038330bf1/foreign/src' installing to /builddir/build/BUILD/R-3.6.0/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done begin installing recommended package KernSmooth * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpgCqh0A/R.INSTALL67ce3a112376/KernSmooth/src' gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c blkest.f -o blkest.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c cp.f -o cp.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dgedi.f -o dgedi.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dgefa.f -o dgefa.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c dgesl.f -o dgesl.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c linbin.f -o linbin.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c linbin2D.f -o linbin2D.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c locpoly.f -o locpoly.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c rlbin.f -o rlbin.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c sdiag.f -o sdiag.o gfortran -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection --no-optimize-sibling-calls -c sstdiag.f -o sstdiag.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -L/builddir/build/BUILD/R-3.6.0/lib -lRblas -L -L -lgfortran -lm -L -L -lgfortran -lm -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpgCqh0A/R.INSTALL67ce3a112376/KernSmooth/src' installing to /builddir/build/BUILD/R-3.6.0/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html bkfe html dpih html dpik html dpill html locpoly html ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) Making 'packages.html' ... done begin installing recommended package rpart * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpG1NrcV/R.INSTALL681421424a3/rpart/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c anova.c -o anova.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c anovapred.c -o anovapred.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c branch.c -o branch.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bsplit.c -o bsplit.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c choose_surg.c -o choose_surg.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fix_cp.c -o fix_cp.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c free_tree.c -o free_tree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gini.c -o gini.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c graycode.c -o graycode.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c insert_split.c -o insert_split.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c make_cp_list.c -o make_cp_list.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c make_cp_table.c -o make_cp_table.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mysort.c -o mysort.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nodesplit.c -o nodesplit.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c partition.c -o partition.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c poisson.c -o poisson.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pred_rpart.c -o pred_rpart.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c print_tree.c -o print_tree.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpart.c -o rpart.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpart_callback.c -o rpart_callback.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpartexp.c -o rpartexp.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpartexp2.c -o rpartexp2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpcountup.c -o rpcountup.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpmatrix.c -o rpmatrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rundown.c -o rundown.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rundown2.c -o rundown2.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c surrogate.c -o surrogate.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c usersplit.c -o usersplit.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c xpred.c -o xpred.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c xval.c -o xval.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpG1NrcV/R.INSTALL681421424a3/rpart/src' installing to /builddir/build/BUILD/R-3.6.0/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder.balance html stagec html summary.rpart html text.rpart html xpred.rpart html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) Making 'packages.html' ... done begin installing recommended package class * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpN7ZUm0/R.INSTALL68a7353f3e72/class/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c class.c -o class.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o class.so class.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpN7ZUm0/R.INSTALL68a7353f3e72/class/src' installing to /builddir/build/BUILD/R-3.6.0/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html batchSOM html condense html knn html knn.cv html knn1 html lvq1 html lvq2 html lvq3 html lvqinit html lvqtest html multiedit html olvq1 html reduce.nn html somgrid html ** building package indices ** testing if installed package can be loaded * DONE (class) Making 'packages.html' ... done begin installing recommended package nnet * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpVyLQtN/R.INSTALL68cc19e121/nnet/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c nnet.c -o nnet.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o nnet.so nnet.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpVyLQtN/R.INSTALL68cc19e121/nnet/src' installing to /builddir/build/BUILD/R-3.6.0/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html nnet html predict.nnet html which.is.max html ** building package indices ** testing if installed package can be loaded * DONE (nnet) Making 'packages.html' ... done begin installing recommended package spatial * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/RtmpfmFPKw/R.INSTALL68f05a9a6050/spatial/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init.c -o init.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c krc.c -o krc.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pps.c -o pps.o gcc -shared -L/builddir/build/BUILD/R-3.6.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o spatial.so init.o krc.o pps.o -L/builddir/build/BUILD/R-3.6.0/lib -lR make[3]: Leaving directory '/tmp/RtmpfmFPKw/R.INSTALL68f05a9a6050/spatial/src' installing to /builddir/build/BUILD/R-3.6.0/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done begin installing recommended package mgcv * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/tmp/Rtmpahx4sR/R.INSTALL691c1ffd802f/mgcv/src' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c coxph.c -o coxph.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c discrete.c -o discrete.o discrete.c: In function 'indReduce': discrete.c:86:32: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized] 86 | double Wij,*Cq,*Aq,*Cq1,*ws,*wl; | ^~ discrete.c:86:28: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized] 86 | double Wij,*Cq,*Aq,*Cq1,*ws,*wl; | ^~ discrete.c: In function 'XWXijs': discrete.c:834:9: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized] 834 | *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli; | ^ discrete.c:834:6: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized] 834 | *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli; | ^ discrete.c:997:27: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized] 997 | pw1) R[1] = -2.0;return; /* signals error */ | ^~ mat.c:1872:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1872 | if (*n>1) R[1] = -2.0;return; /* signals error */ | ^~~~~~ mat.c: In function 'Rlanczos': mat.c:3467:15: warning: 'cir' may be used uninitialized in this function [-Wmaybe-uninitialized] 3467 | #pragma omp parallel private(i,ri) num_threads(*nt) | ^~~ gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c matrix.c -o matrix.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mgcv.c -o mgcv.o gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c misc.c -o misc.o misc.c: In function 'tweedious': misc.c:321:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 321 | if (j_max>j_hi) j_max = j_hi; if (j_maxj_hi) j_max = j_hi; if (j_max BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: compilation terminated. BUILDSTDERR: make[2]: *** [/builddir/build/BUILD/R-3.6.0/etc/Makeconf:167: conftest.o] Error 1 + cd src/nmath/standalone + make random.effects html residuals.gam html rig html rmvn html s html scat html sdiag html single.index html slanczos html smooth.construct html smooth.construct.ad.smooth.spec html smooth.construct.bs.smooth.spec html smooth.construct.cr.smooth.spec html smooth.construct.ds.smooth.spec html smooth.construct.fs.smooth.spec html smooth.construct.gp.smooth.spec html smooth.construct.mrf.smooth.spec html smooth.construct.ps.smooth.spec html smooth.construct.re.smooth.spec html smooth.construct.so.smooth.spec html smooth.construct.sos.smooth.spec html smooth.construct.t2.smooth.spec html smooth.construct.tensor.smooth.spec html smooth.construct.tp.smooth.spec html smooth.terms html smooth2random html smoothCon html sp.vcov html spasm.construct html step.gam html summary.gam html t2 html te html tensor.prod.model.matrix html totalPenaltySpace html trichol html trind.generator html twlss html uniquecombs html vcov.gam html vis.gam html ziP html ziplss html ** building package indices ** testing if installed package can be loaded * DONE (mgcv) Making 'packages.html' ... done make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/Recommended' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library/Recommended' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' building/updating vignettes for package 'grid' ... building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0' configuring Java ... Java interpreter : /usr/bin/java Java version : 10.0.2 Java home path : /usr/lib/jvm/java-10-openjdk-10.0.2.13-7.4.riscv64.fc29.riscv64 Java compiler : not present Java headers gen.: Java archive tool: trying to compile and link a JNI program detected JNI cpp flags : detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm make[2]: Entering directory '/tmp/Rjavareconf.Y0IjCy' gcc -I"/builddir/build/BUILD/R-3.6.0/include" -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c conftest.c -o conftest.o make[2]: Leaving directory '/tmp/Rjavareconf.Y0IjCy' Unable to compile a JNI program JAVA_HOME : /usr/lib/jvm/java-10-openjdk-10.0.2.13-7.4.riscv64.fc29.riscv64 Java library path: JNI cpp flags : JNI linker flags : Updating Java configuration in /builddir/build/BUILD/R-3.6.0 Done. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0' (cd ../../include; make Rmath.h) make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include' make[1]: 'Rmath.h' is up to date. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include' Copying source files make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mlutils.c -o mlutils.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c d1mach.c -o d1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c i1mach.c -o i1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmax2.c -o fmax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmin2.c -o fmin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fprec.c -o fprec.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fround.c -o fround.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ftrunc.c -o ftrunc.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sign.c -o sign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fsign.c -o fsign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imax2.c -o imax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imin2.c -o imin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chebyshev.c -o chebyshev.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c log1p.c -o log1p.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgammacor.c -o lgammacor.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gammalims.c -o gammalims.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stirlerr.c -o stirlerr.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bd0.c -o bd0.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma.c -o gamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgamma.c -o lgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c beta.c -o beta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lbeta.c -o lbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c polygamma.c -o polygamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cospi.c -o cospi.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_i.c -o bessel_i.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_j.c -o bessel_j.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_k.c -o bessel_k.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_y.c -o bessel_y.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c choose.c -o choose.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c snorm.c -o snorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sexp.c -o sexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgamma.c -o dgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgamma.c -o pgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgamma.c -o qgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgamma.c -o rgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbeta.c -o dbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbeta.c -o pbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbeta.c -o qbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbeta.c -o rbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dunif.c -o dunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c punif.c -o punif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qunif.c -o qunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c runif.c -o runif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnorm.c -o dnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnorm.c -o pnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnorm.c -o qnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnorm.c -o rnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlnorm.c -o dlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plnorm.c -o plnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlnorm.c -o qlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlnorm.c -o rlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c df.c -o df.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pf.c -o pf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qf.c -o qf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rf.c -o rf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnf.c -o dnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dt.c -o dt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pt.c -o pt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qt.c -o qt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rt.c -o rt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnt.c -o dnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dchisq.c -o dchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pchisq.c -o pchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qchisq.c -o qchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rchisq.c -o rchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnchisq.c -o rnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbinom.c -o dbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbinom.c -o pbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbinom.c -o qbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbinom.c -o rbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rmultinom.c -o rmultinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dcauchy.c -o dcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pcauchy.c -o pcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qcauchy.c -o qcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rcauchy.c -o rcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dexp.c -o dexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pexp.c -o pexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qexp.c -o qexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rexp.c -o rexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgeom.c -o dgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgeom.c -o pgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgeom.c -o qgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgeom.c -o rgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dhyper.c -o dhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c phyper.c -o phyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qhyper.c -o qhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rhyper.c -o rhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbinom.c -o dnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbinom.c -o pnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbinom.c -o qnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnbinom.c -o rnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dpois.c -o dpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ppois.c -o ppois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qpois.c -o qpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpois.c -o rpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dweibull.c -o dweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pweibull.c -o pweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qweibull.c -o qweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rweibull.c -o rweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlogis.c -o dlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plogis.c -o plogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlogis.c -o qlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlogis.c -o rlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnchisq.c -o dnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnchisq.c -o pnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnchisq.c -o qnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbeta.c -o dnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbeta.c -o pnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbeta.c -o qnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnf.c -o pnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnt.c -o pnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnf.c -o qnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnt.c -o qnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ptukey.c -o ptukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qtukey.c -o qtukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c toms708.c -o toms708.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c wilcox.c -o wilcox.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c signrank.c -o signrank.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c std_unif.c -o std_unif.o ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o ranlib libRmath.a make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mlutils.c -o mlutils.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c d1mach.c -o d1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c i1mach.c -o i1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmax2.c -o fmax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fmin2.c -o fmin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fprec.c -o fprec.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fround.c -o fround.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ftrunc.c -o ftrunc.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sign.c -o sign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fsign.c -o fsign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imax2.c -o imax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c imin2.c -o imin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chebyshev.c -o chebyshev.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c log1p.c -o log1p.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgammacor.c -o lgammacor.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gammalims.c -o gammalims.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stirlerr.c -o stirlerr.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bd0.c -o bd0.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma.c -o gamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lgamma.c -o lgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gamma_cody.c -o gamma_cody.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c beta.c -o beta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c lbeta.c -o lbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c polygamma.c -o polygamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cospi.c -o cospi.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_i.c -o bessel_i.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_j.c -o bessel_j.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_k.c -o bessel_k.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bessel_y.c -o bessel_y.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c choose.c -o choose.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c snorm.c -o snorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sexp.c -o sexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgamma.c -o dgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgamma.c -o pgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgamma.c -o qgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgamma.c -o rgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbeta.c -o dbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbeta.c -o pbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbeta.c -o qbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbeta.c -o rbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dunif.c -o dunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c punif.c -o punif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qunif.c -o qunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c runif.c -o runif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnorm.c -o dnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnorm.c -o pnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnorm.c -o qnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnorm.c -o rnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlnorm.c -o dlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plnorm.c -o plnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlnorm.c -o qlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlnorm.c -o rlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c df.c -o df.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pf.c -o pf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qf.c -o qf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rf.c -o rf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnf.c -o dnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dt.c -o dt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pt.c -o pt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qt.c -o qt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rt.c -o rt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnt.c -o dnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dchisq.c -o dchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pchisq.c -o pchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qchisq.c -o qchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rchisq.c -o rchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnchisq.c -o rnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dbinom.c -o dbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pbinom.c -o pbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qbinom.c -o qbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rbinom.c -o rbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rmultinom.c -o rmultinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dcauchy.c -o dcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pcauchy.c -o pcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qcauchy.c -o qcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rcauchy.c -o rcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dexp.c -o dexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pexp.c -o pexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qexp.c -o qexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rexp.c -o rexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dgeom.c -o dgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pgeom.c -o pgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qgeom.c -o qgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rgeom.c -o rgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dhyper.c -o dhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c phyper.c -o phyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qhyper.c -o qhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rhyper.c -o rhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbinom.c -o dnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbinom.c -o pnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbinom.c -o qnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rnbinom.c -o rnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dpois.c -o dpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ppois.c -o ppois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qpois.c -o qpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rpois.c -o rpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dweibull.c -o dweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pweibull.c -o pweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qweibull.c -o qweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rweibull.c -o rweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dlogis.c -o dlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c plogis.c -o plogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qlogis.c -o qlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rlogis.c -o rlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnchisq.c -o dnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnchisq.c -o pnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnchisq.c -o qnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dnbeta.c -o dnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnbeta.c -o pnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnbeta.c -o qnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnf.c -o pnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pnt.c -o pnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnf.c -o qnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qnt.c -o qnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ptukey.c -o ptukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c qtukey.c -o qtukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c toms708.c -o toms708.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c wilcox.c -o wilcox.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c signrank.c -o signrank.lo BUILDSTDERR: gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenm+ make pdf BUILDSTDERR: Converting parsed Rd's to LaTeX ........................................... BUILDSTDERR: Converting parsed Rd's to LaTeX ...... BUILDSTDERR: Converting parsed Rd's to LaTeX ............... BUILDSTDERR: Converting parsed Rd's to LaTeX ....... BUILDSTDERR: Converting parsed Rd's to LaTeX ....... BUILDSTDERR: Converting parsed Rd's to LaTeX .............................. BUILDSTDERR: Converting parsed Rd's to LaTeX ........ BUILDSTDERR: Converting parsed Rd's to LaTeX ........ BUILDSTDERR: Converting parsed Rd's to LaTeX ......... BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX ............... BUILDSTDERR: Converting parsed Rd's to LaTeX ...... BUILDSTDERR: Converting parsed Rd's to LaTeX ........... BUILDSTDERR: Converting parsed Rd's to LaTeX ............................ BUILDSTDERR: Converting parsed Rd's to LaTeX ........... BUILDSTDERR: Converting parsed Rd's to LaTeX ........ BUILDSTDERR: Converting parsed Rd's to LaTeX ..... BUILDSTDERR: Converting parsed Rd's to LaTeX BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX BUILDSTDERR: Converting parsed Rd's to LaTeX .. BUILDSTDERR: Converting parsed Rd's to LaTeX . BUILDSTDERR: Converting parsed Rd's to LaTeX BUILDSTDERR: Converting parsed Rd's to LaTeX .. BUILDSTDERR: Converting parsed Rd's to LaTeX .............. p -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c std_unif.c -o std_unif.lo gcc -shared -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libRmath.so mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath/standalone' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... collecting LaTeX docs for package 'tools' ... collecting LaTeX docs for package 'utils' ... collecting LaTeX docs for package 'grDevices' ... collecting LaTeX docs for package 'graphics' ... collecting LaTeX docs for package 'stats' ... collecting LaTeX docs for package 'datasets' ... collecting LaTeX docs for package 'methods' ... collecting LaTeX docs for package 'grid' ... collecting LaTeX docs for package 'splines' ... collecting LaTeX docs for package 'stats4' ... collecting LaTeX docs for package 'tcltk' ... collecting LaTeX docs for package 'compiler' ... collecting LaTeX docs for package 'parallel' ... collecting LaTeX docs for package 'MASS' ... collecting LaTeX docs for package 'lattice' ... collecting LaTeX docs for package 'Matrix' ... collecting LaTeX docs for package 'nlme' ... collecting LaTeX docs for package 'survival' ... collecting LaTeX docs for package 'boot' ... collecting LaTeX docs for package 'cluster' ... collecting LaTeX docs for package 'codetools' ... collecting LaTeX docs for package 'foreign' ... collecting LaTeX docs for package 'KernSmooth' ... collecting LaTeX docs for package 'rpart' ... collecting LaTeX docs for package 'class' ... collecting LaTeX docs for package 'nnet' ... collecting LaTeX docs for package 'spatial' ... collecting LaTeX docs for package 'mgcv' ... PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-04-01> patch level 5 (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 377. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texliv e/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [1] [2] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [3] [4] Underfull \hbox (badness 6995) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] [9] [10] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 2671) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1953--1953 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2392--2397 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 5019--5021 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6175--6175 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [91] [92] [93] [94] [95] [96] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6584--6586 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6732--6735 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. 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If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [101] Underfull \hbox (badness 3568) in paragraph at lines 6976--6983 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] Underfull \hbox (badness 1077) in paragraph at lines 7293--7299 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7293--7299 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7634--7638 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [112] Underfull \hbox (badness 2351) in paragraph at lines 7752--7755 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [113] [114] [115] [116] [117] Underfull \hbox (badness 4479) in paragraph at lines 8078--8088 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 1629) in paragraph at lines 8525--8537 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 1178) in paragraph at lines 9260--9264 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1735) in paragraph at lines 10408--10412 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [150] [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 6396) in paragraph at lines 10847--10855 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 1946) in paragraph at lines 10847--10855 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 4569) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11963--11967 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] Underfull \hbox (badness 2253) in paragraph at lines 13626--13628 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [195] Underfull \hbox (badness 1565) in paragraph at lines 13697--13701 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [196] Underfull \hbox (badness 4927) in paragraph at lines 13741--13743 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4 /m/n/10 fsep = [197] Underfull \hbox (badness 3148) in paragraph at lines 13834--13839 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [198] Underfull \hbox (badness 1466) in paragraph at lines 13881--13884 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [199] Underfull \hbox (badness 10000) in paragraph at lines 14000--14004 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14011--14014 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [200] [201] [202] [203] Underfull \hbox (badness 3965) in paragraph at lines 14301--14305 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] Underfull \hbox (badness 4429) in paragraph at lines 15076--15079 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [216] [217] Underfull \hbox (badness 10000) in paragraph at lines 15198--15202 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 2426) in paragraph at lines 15198--15202 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want Underfull \hbox (badness 2035) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 within [218] [219] [220] [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 2452) in paragraph at lines 15829--15833 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15829--15833 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [227] [228] [229] Underfull \hbox (badness 1092) in paragraph at lines 16002--16007 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [230] [231] [232] Underfull \hbox (badness 6741) in paragraph at lines 16252--16256 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [233] [234] [235] [236] [237] [238] [239] [240] Underfull \vbox (badness 10000) has occurred while \output is active [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] Underfull \hbox (badness 1478) in paragraph at lines 17541--17544 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [251] [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 17796--17798 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1442) in paragraph at lines 18396--18398 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [263] Underfull \hbox (badness 2452) in paragraph at lines 18488--18504 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1248) in paragraph at lines 18907--18910 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [270] [271] [272] [273] Underfull \hbox (badness 4739) in paragraph at lines 19165--19167 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [274] [275] [276] [277] [278] [279] [280] Underfull \hbox (badness 1596) in paragraph at lines 19584--19589 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [281] [282] [283] [284] [285] [286] [287] [288] [289] Underfull \hbox (badness 2469) in paragraph at lines 20188--20193 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and [290] Underfull \hbox (badness 10000) in paragraph at lines 20202--20209 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 10000) in paragraph at lines 20276--20280 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20276--20280 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [291] [292] [293] Underfull \hbox (badness 1014) in paragraph at lines 20446--20451 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 1264) in paragraph at lines 21235--21240 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [305] Underfull \hbox (badness 4441) in paragraph at lines 21264--21267 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] Underfull \hbox (badness 6047) in paragraph at lines 22011--22013 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) == [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] Underfull \hbox (badness 1077) in paragraph at lines 23052--23058 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 2790) in paragraph at lines 23548--23551 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23548--23551 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [340] [341] [342] [343] Underfull \hbox (badness 1194) in paragraph at lines 23830--23833 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [344] [345] Underfull \hbox (badness 2368) in paragraph at lines 24036--24042 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24036--24042 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 24418--24421 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [352] [353] [354] [355] [356] [357] [358] [359] [360] Underfull \hbox (badness 10000) in paragraph at lines 25023--25025 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 1038) in paragraph at lines 25863--25871 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1735) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25872--25875 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [373] Underfull \hbox (badness 2142) in paragraph at lines 26032--26036 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [374] Underfull \hbox (badness 1968) in paragraph at lines 26082--26087 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26383--26386 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26409--26411 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [378] Underfull \hbox (badness 10000) in paragraph at lines 26444--26449 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 2529) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and Underfull \hbox (badness 7203) in paragraph at lines 26462--26465 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26486--26491 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26486--26491 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 10000) in paragraph at lines 27004--27007 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [386] Underfull \hbox (badness 7925) in paragraph at lines 27083--27087 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27083--27087 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27088--27097 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 2726) in paragraph at lines 27809--27812 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] Underfull \hbox (badness 1533) in paragraph at lines 29500--29503 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [423] [424] Underfull \hbox (badness 1163) in paragraph at lines 29663--29674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 10000) in paragraph at lines 31209--31213 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 31209--31213 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [447] Underfull \hbox (badness 6188) in paragraph at lines 31231--31233 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [448] [449] [450] [451] [452] [453] [454] [455] Underfull \hbox (badness 1655) in paragraph at lines 31787--31789 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] Underfull \hbox (badness 2261) in paragraph at lines 32906--32911 []\T1/ptm/m/n/10 If \T1/zi4/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 [472] Underfull \hbox (badness 10000) in paragraph at lines 32933--32939 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 32933--32939 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] Underfull \hbox (badness 1072) in paragraph at lines 36075--36079 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 36080--36084 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', [517] Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 36120--36127 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [518] [519] [520] [521] [522] Underfull \hbox (badness 1142) in paragraph at lines 36473--36479 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1565) in paragraph at lines 37746--37748 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 4967) in paragraph at lines 38345--38350 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [551] [552] Underfull \hbox (badness 1616) in paragraph at lines 38458--38463 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [553] [554] [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1472) in paragraph at lines 38984--38987 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] Underfull \hbox (badness 10000) in paragraph at lines 39898--39902 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [574] [575] [576] [577] Underfull \hbox (badness 10000) in paragraph at lines 40149--40152 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [578] [579] [580] Underfull \hbox (badness 10000) in paragraph at lines 40333--40337 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [581] [582] [583] [584] [585] [586] [587] [588] Underfull \hbox (badness 10000) in paragraph at lines 40946--40949 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [589] [590] [591] [592] [593] Underfull \vbox (badness 10000) has occurred while \output is active [594] [595] [596] [597] [598] [599] [600] [601] Underfull \hbox (badness 1990) in paragraph at lines 41849--41857 []\T1/zi4/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 4846) in paragraph at lines 41849--41857 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [602] [603] [604] [605] [606] [607] [608] Underfull \hbox (badness 1917) in paragraph at lines 42355--42362 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [609] [610] [611] [612] [613] [614] [615] [616] [617] [618] Underfull \hbox (badness 3668) in paragraph at lines 43084--43086 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [619] [620] Underfull \hbox (badness 2401) in paragraph at lines 43212--43216 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [621] [622] [623] Underfull \hbox (badness 2111) in paragraph at lines 43401--43406 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 10000) in paragraph at lines 43422--43427 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 5417) in paragraph at lines 44004--44008 []\T1/zi4/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 [632] Underfull \hbox (badness 10000) in paragraph at lines 44065--44069 []\T1/zi4/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 [633] [634]) (./compiler-pkg.tex Chapter 2. [635] [636] [637] [638]) (./datasets-pkg.tex Chapter 3. [639] [640] [641] [642] [643] [644] Underfull \vbox (badness 1472) has occurred while \output is active [645] [646] [647] [648] [649] [650] [651] [652] [653] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] Overfull \vbox (4.26088pt too high) has occurred while \output is active [676] [677] [678] [679] [680] [681] Overfull \vbox (13.87083pt too high) has occurred while \output is active [682] Underfull \vbox (badness 2376) has occurred while \output is active [683] [684] Overfull \vbox (12.25539pt too high) has occurred while \output is active [685] [686] Overfull \vbox (17.12102pt too high) has occurred while \output is active [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] Overfull \vbox (10.49593pt too high) has occurred while \output is active [698] Overfull \vbox (15.49593pt too high) has occurred while \output is active [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713]) (./grDevices-pkg.tex [714] Chapter 4. [715] [716] [717] [718] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [732] [733] [734] Underfull \hbox (badness 1852) in paragraph at lines 1322--1325 []\T1/zi4/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 [735] [736] [737] Underfull \hbox (badness 1490) in paragraph at lines 1528--1533 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [738] [739] [740] [741] [742] [743] Underfull \hbox (badness 1325) in paragraph at lines 1934--1944 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [744] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [745] [746] [747] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [748] [749] [750] [751] [752] [753] [754] [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [765] [766] [767] [768] [769] [770] Underfull \hbox (badness 10000) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4514--4519 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [781] [782] Underfull \hbox (badness 1067) in paragraph at lines 4668--4675 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [783] [784] [785] [786] Underfull \hbox (badness 1377) in paragraph at lines 4971--4976 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [787] Underfull \hbox (badness 1418) in paragraph at lines 5047--5054 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , [788] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [789] Underfull \hbox (badness 1377) in paragraph at lines 5176--5181 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [790] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [791] [792] Underfull \hbox (badness 2035) in paragraph at lines 5380--5389 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [793] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5448--5455 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [794] [795] Underfull \hbox (badness 1546) in paragraph at lines 5590--5598 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 6125--6128 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [816] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [817] [818] [819] [820] [821] Underfull \hbox (badness 3780) in paragraph at lines 7345--7351 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [822] [823] Underfull \hbox (badness 2680) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [824] [825] [826]) (./graphics-pkg.tex Chapter 5. [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] Underfull \vbox (badness 10000) has occurred while \output is active [842] [843] [844] [845] [846] Underfull \hbox (badness 4634) in paragraph at lines 1349--1352 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] Underfull \hbox (badness 1009) in paragraph at lines 2388--2395 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [863] [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \vbox (badness 10000) has occurred while \output is active [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 3229) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [896] [897] [898] [899] [900] Underfull \hbox (badness 10000) in paragraph at lines 4889--4895 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4889--4895 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [901] Underfull \hbox (badness 10000) in paragraph at lines 5020--5023 [902] Underfull \hbox (badness 10000) in paragraph at lines 5081--5083 [903 ] [904 ] [905] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750 [][] [928 ] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Underfull \hbox (badness 2012) in paragraph at lines 7574--7577 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi nt [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 8834--8836 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [960]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8916 \HeaderA{units}{Graphical Units}{units} [961] [962] [963] [964]) (./grid-pkg.tex Chapter 6. [965] [966] [967] [968] [969] [970] [971] [972] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [973] [974] [975] [976] [977] [978] [979] [980] [981] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] Underfull \vbox (badness 10000) has occurred while \output is active [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1035] [1036] [1037] [1038] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1067] [1068] [1069] [1070]) (./methods-pkg.tex Chapter 7. [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \vbox (badness 10000) has occurred while \output is active [1079] Underfull \vbox (badness 10000) has occurred while \output is active [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1097] [1098] [1099] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1105] [1106] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1107] [1108] [1109] [1110] [1111] [1112] [1113] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1114] [1115] [1116] [1117] [1118] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1119] [1120] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Underfull \vbox (badness 10000) has occurred while \output is active [1139] Underfull \vbox (badness 10000) has occurred while \output is active [1140] [1141] [1142] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1143] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1144] [1145] [1146] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1155] [1156] [1157] [1158] Underfull \vbox (badness 10000) has occurred while \output is active [1159] [1160] [1161]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1162] [1163] [1164]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1165] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1166] [1167] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1201] [1202] [1203] [1204] [1205] [1206] [1207] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1208] [1209] [1210]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1231] [1232]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246]) (./stats-pkg.tex Chapter 10. [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] Underfull \hbox (badness 2503) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 1127) in paragraph at lines 4349--4352 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 3989) in paragraph at lines 4679--4686 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 2556) in paragraph at lines 5315--5318 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5332--5334 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1325] [1326] [1327] [1328] [1329] [1330] Underfull \hbox (badness 2503) in paragraph at lines 5724--5728 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 7081) in paragraph at lines 6518--6521 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6522--6524 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7367--7370 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] Underfull \vbox (badness 10000) has occurred while \output is active [1377] [1378] [1379] [1380] Underfull \hbox (badness 2626) in paragraph at lines 9044--9047 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1381] [1382] Underfull \hbox (badness 2503) in paragraph at lines 9151--9155 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 4518) in paragraph at lines 10461--10466 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 2142) in paragraph at lines 10821--10824 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10840--10843 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1407] Underfull \hbox (badness 1708) in paragraph at lines 10902--10906 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 1694) in paragraph at lines 11298--11301 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1413] [1414] [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 11625--11628 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of Underfull \hbox (badness 1281) in paragraph at lines 11625--11628 \T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia l ap-prox-i-ma-tion may be con-sid-er-ably [1419] [1420]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11779 \aliasA{hat}{influence.measures}{hat} [1421] [1422] Underfull \hbox (badness 1484) in paragraph at lines 11914--11916 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 10000) in paragraph at lines 12507--12509 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit = [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2894) in paragraph at lines 12843--12847 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 13593--13598 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] Underfull \hbox (badness 4518) in paragraph at lines 14245--14250 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1458] [1459] Underfull \hbox (badness 8151) in paragraph at lines 14383--14387 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14390--14392 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] Underfull \hbox (badness 2503) in paragraph at lines 15461--15465 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1477] [1478] [1479] [1480] [1481] [1482] [1483] Underfull \hbox (badness 4621) in paragraph at lines 15973--15979 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/ ptm/m/n/10 and [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] Underfull \vbox (badness 10000) has occurred while \output is active [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1377) in paragraph at lines 18567--18572 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18572--18575 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 18585--18589 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18585--18589 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to [1524] Underfull \hbox (badness 2662) in paragraph at lines 18593--18597 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18818--18818 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18821--18821 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1528] [1529] [1530] [1531] [1532] [1533] Underfull \hbox (badness 1337) in paragraph at lines 19243--19246 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 3049) in paragraph at lines 19739--19743 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1543] [1544] [1545] [1546] Underfull \hbox (badness 1194) in paragraph at lines 19997--20000 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 20372--20375 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1552] Underfull \hbox (badness 3919) in paragraph at lines 20399--20401 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] Underfull \hbox (badness 10000) in paragraph at lines 21476--21482 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Underfull \hbox (badness 1337) in paragraph at lines 22823--22829 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23388--23388 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1599] [1600] [1601] Underfull \hbox (badness 10000) in paragraph at lines 23639--23642 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23639--23642 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 10000) in paragraph at lines 24224--24227 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] = [1611] Underfull \hbox (badness 3690) in paragraph at lines 24276--24280 [][][]\T1/zi4/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 [1612] [1613] [1614] [1615] [1616] [1617] [1618] Underfull \hbox (badness 2165) in paragraph at lines 24753--24758 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1619] [1620] [1621] [1622] Underfull \hbox (badness 1867) in paragraph at lines 24958--24960 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24971--24975 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \vbox (badness 10000) has occurred while \output is active [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \hbox (badness 3514) in paragraph at lines 26510--26515 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] [1646] [1647] [1648] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26744--26744 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1649] Underfull \hbox (badness 3514) in paragraph at lines 26780--26786 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1650] [1651] [1652] Underfull \hbox (badness 3514) in paragraph at lines 26994--26999 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1653] [1654] Underfull \hbox (badness 3514) in paragraph at lines 27081--27086 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1655] Underfull \hbox (badness 3514) in paragraph at lines 27146--27151 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1656] Underfull \hbox (badness 3514) in paragraph at lines 27240--27245 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1657] [1658] Underfull \hbox (badness 6691) in paragraph at lines 27332--27337 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 4024) in paragraph at lines 27862--27865 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 5431) in paragraph at lines 28468--28470 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1676] [1677] [1678] [1679] Underfull \hbox (badness 5431) in paragraph at lines 28678--28681 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1680] [1681] [1682] [1683] [1684] Underfull \hbox (badness 1337) in paragraph at lines 28992--28996 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1685] [1686] [1687] [1688] Underfull \hbox (badness 1616) in paragraph at lines 29294--29297 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1689] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] Underfull \hbox (badness 3557) in paragraph at lines 30424--30428 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4 /m/n/10 interval = [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] [1710] [1711] Underfull \hbox (badness 1337) in paragraph at lines 30788--30792 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719] Underfull \hbox (badness 1337) in paragraph at lines 31315--31319 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728]) (./stats4-pkg.tex Chapter 11. [1729] [1730] [1731] [1732] [1733] [1734]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1735] [1736] [1737]) (./tcltk-pkg.tex [1738] Chapter 12. [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758]) (./tools-pkg.tex Chapter 13. [1759] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1760] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1761] [1762] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1763] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1764] [1765] [1766] [1767] [1768] [1769] [1770] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1776] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1777] [1778] [1779] [1780] [1781] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1782] [1783] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1784] Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1785] [1786] [1787]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1788] [1789] [1790] [1791] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1792] [1793] [1794] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1795] [1796] [1797] [1798] [1799] [1800] [1801] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2837. [1802] [1803] [1804] [1805] Underfull \hbox (badness 1424) in paragraph at lines 3119--3121 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] Underfull \hbox (badness 10000) in paragraph at lines 3823--3825 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1816] [1817] Underfull \hbox (badness 10000) in paragraph at lines 3962--3965 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1818] Underfull \hbox (badness 1137) in paragraph at lines 4064--4066 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1819] [1820] [1821] [1822] [1823] Underfull \hbox (badness 1796) in paragraph at lines 4372--4377 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type == [1824] Underfull \hbox (badness 1838) in paragraph at lines 4446--4452 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4446--4452 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1825] [1826] [1827] Underfull \hbox (badness 2197) in paragraph at lines 4662--4672 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : [1828] Underfull \hbox (badness 1571) in paragraph at lines 4725--4729 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1829] [1830] [1831]) (./utils-pkg.tex [1832] Chapter 14. Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1838] [1839] [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1843] [1844] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1845] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1846] [1847] [1848] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1865] [1866] [1867] [1868] [1869]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.clipboard}) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [1870] [1871] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1872] [1873] [1874] [1875] [1876] [1877] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](...,header = TRUE,sep = [1878] [1879] [1880] [1881] [1882] [1883] [1884] [1885] [1886] [1887] [1888] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1889] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1890] [1891] Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.format}) has been a lready used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] Underfull \hbox (badness 1371) in paragraph at lines 5996--5998 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1919] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1923] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1924] [1925] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1926] [1927] Underfull \hbox (badness 1325) in paragraph at lines 6632--6636 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [1928] Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1929] Underfull \hbox (badness 3219) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6792--6799 [][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [1930] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from [1954] Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [1962] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] Underfull \vbox (badness 5533) has occurred while \output is active [1972] [1973] [1974] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1975] [1976] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1985] Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 11163--11167 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able [1998] Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [1999] [2000] [2001] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2002] [2003] [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2006] [2007] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2008] Underfull \hbox (badness 4779) in paragraph at lines 12237--12239 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a nd Underfull \hbox (badness 1077) in paragraph at lines 12267--12274 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 3780) in paragraph at lines 12668--12672 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 12684--12687 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2015] [2016] [2017] Underfull \hbox (badness 2302) in paragraph at lines 12889--12891 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13185--13190 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13194--13197 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2023] Underfull \vbox (badness 10000) has occurred while \output is active [2024] [2025] [2026] [2027] [2028] Underfull \hbox (badness 2932) in paragraph at lines 13614--13621 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 13614--13621 \T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [2029] [2030] [2031] [2032] Underfull \hbox (badness 6510) in paragraph at lines 13923--13927 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 13930--13933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 13930--13933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 14594--14599 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 14594--14599 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and [2042] Underfull \hbox (badness 1052) in paragraph at lines 14600--14602 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 14659--14662 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] Underfull \hbox (badness 10000) in paragraph at lines 15432--15434 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/zi4/m/sl/10 file = [2055] [2056] [2057]) [2058] [2059] [2060] (./KernSmooth-pkg.tex Chapter 15. [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070]) (./MASS-pkg.tex Chapter 16. [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] Underfull \hbox (badness 7944) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [2108] [2109] [2110] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm /m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative [2111] [2112] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] Underfull \hbox (badness 1117) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2138] Underfull \hbox (badness 1117) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2156] [2157] [2158] [2159] [2160] Underfull \vbox (badness 10000) has occurred while \output is active [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] Underfull \hbox (badness 1117) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2169] Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2170] [2171] [2172] Underfull \hbox (badness 6775) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]) (./Matrix-pkg.tex 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 [2219] 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 [2220] [2221] [2222] [2223] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2224] [2225] Underfull \hbox (badness 2418) in paragraph at lines 597--600 []\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2226] [2227] [2228] [2229] [2230] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a-lently, \T1/zi4/m/sl/10 to = [2231] [2232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} Underfull \hbox (badness 1117) in paragraph at lines 1189--1195 \T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t he same al-go-rithm [2233pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol ,dsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works via] [2234] [2235] Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2236] [2237] Underfull \hbox (badness 1097) in paragraph at lines 1560--1563 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2238]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2239] [2240] [2241] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2242] [2243] [2244] [2245] [2246] Underfull \hbox (badness 1360) in paragraph at lines 2295--2299 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via [2247] [2248] [2249] [2250] Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble [2251] [2252] Underfull \hbox (badness 6842) in paragraph at lines 2700--2703 []\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2253] Underfull \hbox (badness 10000) in paragraph at lines 2986--2990 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro up meth-ods re-turn a [2254] [2255] [2256] Underfull \hbox (badness 1173) in paragraph at lines 3196--3198 []\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2257] [2258] Underfull \hbox (badness 1354) in paragraph at lines 3442--3445 []\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex -plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in -her-it-ing from [2259] [2260] [2261] [2262] [2263] Underfull \hbox (badness 6188) in paragraph at lines 3852--3855 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = Underfull \hbox (badness 5147) in paragraph at lines 3855--3858 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = [2264] [2265] Underfull \hbox (badness 2318) in paragraph at lines 3969--3973 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2266] [2267] Underfull \hbox (badness 5245) in paragraph at lines 4105--4109 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1 0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x) [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (3.77782pt too wide) in paragraph at lines 4527--4527 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (48.77782pt too wide) in paragraph at lines 4530--4530 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2274] [2275] Underfull \hbox (badness 1931) in paragraph at lines 4762--4764 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2276] [2277] [2278] [2279] [2280] Underfull \hbox (badness 1005) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA \T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1655) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4 /m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2281] Overfull \hbox (42.75635pt too wide) in paragraph at lines 5134--5134 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2282] Underfull \hbox (badness 3229) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2283] Underfull \hbox (badness 4995) in paragraph at lines 5282--5285 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 5292--5295 []\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional [2284] [2285] [2286] [2287] [2288] Underfull \hbox (badness 1014) in paragraph at lines 5669--5672 []\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10 is a tri-an-gu-lar ma-trix. Anal-o-gously, [2289] [2290] [2291] [2292] Underfull \hbox (badness 10000) in paragraph at lines 5984--5987 []\T1/zi4/m/sl/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 [2293] Underfull \hbox (badness 2478) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2294] Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2295] Underfull \hbox (badness 10000) in paragraph at lines 6296--6299 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2296] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2297] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2298] Underfull \hbox (badness 2050) in paragraph at lines 6545--6548 []\T1/zi4/m/sl/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 [2299] [2300] [2301] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2302] Underfull \hbox (badness 6268) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2303]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1527) in paragraph at lines 6961--6963 []\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \ T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 6966--6969 []\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 [2304]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2305pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod.Rdash.methods}) has be en already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 ] [2306] Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 1448) in paragraph at lines 7426--7431 \T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 1264) in paragraph at lines 7441--7442 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures, see [2307] [2308] Underfull \hbox (badness 1430) in paragraph at lines 7585--7590 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2309] Underfull \hbox (badness 10000) in paragraph at lines 7656--7659 []\T1/zi4/m/sl/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 [2310] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X [2311] [2312] Underfull \vbox (badness 10000) has occurred while \output is active [2313] Underfull \hbox (badness 2478) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2314] [2315] Underfull \hbox (badness 5924) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim-ple meth-ods [2316]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2317] [2318] Underfull \hbox (badness 10000) in paragraph at lines 8427--8430 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2319] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2320] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2321] Underfull \vbox (badness 10000) has occurred while \output is active [2322] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 8724--8727 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low [2323] [2324] [2325] [2326]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2327] [2328] [2329] [2330]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.rcond}) has been already u sed, duplicate ignored \relax l.9252 ... the Reciprocal Condition Number}{rcond} [2331] [2332] [2333] [2334] Underfull \hbox (badness 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1852) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][]( nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 --- Underfull \hbox (badness 2343) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.solve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} [2339] Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse = [2340] Underfull \hbox (badness 4403) in paragraph at lines 10053--10056 []\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing \T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame [2341] Underfull \hbox (badness 10000) in paragraph at lines 10159--10162 []\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co -er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] Underfull \hbox (badness 10000) in paragraph at lines 10758--10766 []\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 10758--10766 \T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [2350]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2351] [2352] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2353] [2354] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2355] Underfull \vbox (badness 10000) has occurred while \output is active [2356] [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/ sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be [2359] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2360] [2361] Underfull \hbox (badness 1831) in paragraph at lines 11740--11746 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2362] Underfull \hbox (badness 1902) in paragraph at lines 11775--11779 []\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a nd other [2363] [2364] [2365] [2366] [2367] [2368] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2369] [2370] [2371]) (./boot-pkg.tex [2372] Chapter 18. [2373] [2374] [2375] [2376] [2377] [2378] [2379] [2380] [2381] [2382] Underfull \hbox (badness 1297) in paragraph at lines 797--807 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour [2383] 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. [2384] Underfull \vbox (badness 10000) has occurred while \output is active [2385] [2386] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 1859) in paragraph at lines 1066--1070 \T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will [2387] 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 [2388] [2389] [2390] [2391] 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- [2392] [2393] [2394] [2395] [2396] [2397] Underfull \hbox (badness 1005) in paragraph at lines 1797--1804 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2398] [2399] Underfull \vbox (badness 10000) has occurred while \output is active [2400] Underfull \hbox (badness 7379) 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. [2401] [2402] [2403] [2404] 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 [2405] 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. [2406] [2407] Underfull \hbox (badness 2970) 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/zi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] 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 [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] 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 [2442] [2443] [2444] [2445] 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 [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] [2455] [2456] Underfull \hbox (badness 4954) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475]) (./class-pkg.tex [2476] Chapter 19. [2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492]) (./cluster-pkg.tex Chapter 20. [2493] [2494] [2495] [2496] [2497] Underfull \vbox (badness 7777) has occurred while \output is active [2498] [2499] [2500] [2501] [2502] Underfull \hbox (badness 4144) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2506] [2507] Underfull \hbox (badness 10000) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2508] [2509] [2510] Underfull \hbox (badness 6110) in paragraph at lines 1189--1193 []\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2511] [2512] [2513] Underfull \hbox (badness 10000) in paragraph at lines 1458--1461 [2514] [2515] Underfull \hbox (badness 2503) in paragraph at lines 1570--1573 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 2161--2164 Underfull \hbox (badness 10000) in paragraph at lines 2175--2181 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2524] [2525] [2526] [2527] Underfull \hbox (badness 6675) in paragraph at lines 2410--2412 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2528] [2529] [2530] [2531] [2532] [2533] [2534] Underfull \hbox (badness 2980) in paragraph at lines 2901--2905 [][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2535] [2536] [2537] [2538] [2539] Underfull \hbox (badness 1142) in paragraph at lines 3242--3245 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2540] [2541] Underfull \hbox (badness 1142) in paragraph at lines 3361--3364 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2542] [2543] [2544] [2545] Underfull \hbox (badness 2582) in paragraph at lines 3584--3589 [][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2546] Underfull \hbox (badness 3209) in paragraph at lines 3646--3651 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi 4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which Underfull \hbox (badness 8019) in paragraph at lines 3646--3651 \T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/ m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx [2547] [2548] [2549] [2550] Underfull \hbox (badness 10000) in paragraph at lines 3938--3940 []\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2551] [2552] [2553] [2554] Underfull \hbox (badness 2626) in paragraph at lines 4162--4167 []\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col = [2555] Underfull \hbox (badness 1383) in paragraph at lines 4240--4245 []\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2556] [2557] [2558] [2559] [2560] [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 4668--4670 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2563]) (./codetools-pkg.tex [2564] Chapter 21. [2565] [2566] [2567] [2568] [2569]) (./foreign-pkg.tex [2570] Chapter 22. [2571] [2572] [2573] [2574] [2575] [2576] [2577] [2578] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de -fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to [2579] Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 813--814 [2583] [2584] [2585] [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2590] [2591]) (./lattice-pkg.tex [2592] Chapter 23. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2609] Underfull \vbox (badness 4416) has occurred while \output is active [2610] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2611] [2612] [2613] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to 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 [2614] [2615] [2616] [2617] [2618] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, the value of [2619] [2620] [2621] [2622] [2623] [2624] [2625] [2626] [2627] [2628] Underfull \hbox (badness 2781) in paragraph at lines 2848--2850 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2629] Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2630] [2631] [2632] [2633] [2634] [2635] [2636]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.parallel}) has been already used, duplic ate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} [2637] [2638] [2639] [2640] [2641] [2642] [2643] Underfull \hbox (badness 5696) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2644] [2645] Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2646] [2647] [2648] Underfull \hbox (badness 3492) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2649] [2650] [2651] [2652] [2653] [2654] [2655] [2656] [2657] [2658] Underfull \hbox (badness 6157) in paragraph at lines 5035--5038 []\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2659] [2660] [2661] [2662] [2663] [2664] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5486--5489 \T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2665] [2666] [2667] [2668] [2669] Underfull \hbox (badness 4805) in paragraph at lines 5846--5850 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5857--5864 \T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5857--5864 [][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2670] [2671] [2672] [2673] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6157--6162 \T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2674] [2675] Underfull \hbox (badness 2310) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 3168) in paragraph at lines 7055--7059 \T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U se [2687] [2688] [2689] [2690] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2691] [2692] Underfull \hbox (badness 3333) in paragraph at lines 7498--7500 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2693] [2694] [2695] Underfull \vbox (badness 10000) has occurred while \output is active [2696] [2697] [2698] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2707] Underfull \hbox (badness 1092) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2708] [2709] Underfull \hbox (badness 3895) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2710] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2711] [2712] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 8876--8879 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2713] [2714] [2715] [2716] Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4 /m/sl/10 left,right,left.name,right.name,condition [2717] [2718] [2719] [2720] [2721] [2722] [2723] Underfull \hbox (badness 2310) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2724] [2725] [2726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2727] [2728] [2729] Underfull \hbox (badness 4144) in paragraph at lines 10077--10080 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10077--10080 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2730] [2731]) (./mgcv-pkg.tex [2732] Chapter 24. [2733] [2734] [2735] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2736] [2737] [2738] [2739] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/ n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 365--372 [][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][] []\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][] \T1/ptm/m/n/10 , [2740] [2741] [2742] [2743] [2744] [2745] [2746] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2747] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2748] Underfull \vbox (badness 10000) has occurred while \output is active [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] Underfull \hbox (badness 1142) in paragraph at lines 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2772] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2773] [2774] [2775] [2776] [2777] Underfull \vbox (badness 10000) has occurred while \output is active [2778] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \vbox (badness 10000) has occurred while \output is active [2780] [2781] [2782] [2783] [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2794] [2795] Underfull \vbox (badness 10000) has occurred while \output is active [2796] [2797] [2798] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2799] [2800] [2801] [2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2811] Underfull \hbox (badness 1231) in paragraph at lines 4692--4694 []\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with [2812] [2813] [2814] Underfull \vbox (badness 10000) has occurred while \output is active [2815] [2816] [2817] Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 10000) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(... ,fit=FALSE) \T1/ptm/m/n/10 or [2825] [2826] Underfull \vbox (badness 10000) has occurred while \output is active [2827] [2828] [2829] [2830] [2831] [2832] [2833] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2834] [2835] [2836] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] Underfull \hbox (badness 1087) in paragraph at lines 6326--6327 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas e, and if [2841] [2842] [2843] Underfull \vbox (badness 10000) has occurred while \output is active [2844] Underfull \vbox (badness 10000) has occurred while \output is active [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] [2867] Underfull \hbox (badness 6001) in paragraph at lines 7912--7914 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] Underfull \hbox (badness 1038) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2880] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] Underfull \hbox (badness 1852) in paragraph at lines 9387--9390 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2892] [2893] [2894] Underfull \hbox (badness 1852) in paragraph at lines 9551--9554 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2895] [2896] Underfull \vbox (badness 10000) has occurred while \output is active [2897] [2898] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2899] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2900] [2901] [2902] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2903] [2904] [2905] [2906] Underfull \hbox (badness 4792) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/ 10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m /n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2907] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1 0 "deviance"\T1/ptm/m/n/10 , [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [2919] [2920] Underfull \hbox (badness 1320) in paragraph at lines 11084--11089 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T 1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If ma- [2921] [2922] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2923] Underfull \hbox (badness 1762) in paragraph at lines 11279--11291 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Underfull \hbox (badness 7667) in paragraph at lines 11491--11497 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2934] [2935] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2936] [2937] Underfull \hbox (badness 1436) in paragraph at lines 12074--12081 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2938] [2939] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 12754--12760 \T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T 1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] [2955] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2956] [2957] [2958] [2959] Underfull \hbox (badness 3895) in paragraph at lines 13358--13361 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2960] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2961] [2962] [2963] [2964] Underfull \hbox (badness 1371) in paragraph at lines 13620--13626 []\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de fined.smooth[][][]\T1/ptm/m/n/10 , Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4 /m/sl/10 factor.smooth.interaction[][][] [2965] [2966] [2967] [2968] Underfull \hbox (badness 2326) in paragraph at lines 13865--13872 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2969] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978] [2979] [2980] Underfull \vbox (badness 10000) has occurred while \output is active [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] Underfull \hbox (badness 1796) in paragraph at lines 15594--15597 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2997] [2998] [2999] [3000] [3001] [3002]) (./nlme-pkg.tex Chapter 25. [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 2875) in paragraph at lines 1994--2000 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 2256--2262 [][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 1067) in paragraph at lines 4414--4419 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3070] [3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [3082] [3083] [3084] [3085] [3086] [3087] [3088] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [3089] [3090] [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 10000) in paragraph at lines 5973--5978 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [3096] [3097] [3098] [3099] Underfull \hbox (badness 1490) in paragraph at lines 6243--6254 [][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [3100] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3101] [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3107] [3108] [3109] [3110] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [3111] [3112] [3113] [3114] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3134]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig ma}) has been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3135] [3136] [3137] [3138] Underfull \hbox (badness 10000) in paragraph at lines 8802--8809 [][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [3147] [3148] [3149] [3150] [3151]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3164] [3165] Underfull \hbox (badness 1490) in paragraph at lines 10597--10603 [][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1286) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] Underfull \hbox (badness 1067) in paragraph at lines 15888--15893 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3244] [3245] [3246] [3247] Underfull \hbox (badness 1448) in paragraph at lines 16131--16140 \T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3248] [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3258] [3259] [3260] [3261] [3262] Underfull \hbox (badness 8056) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural Underfull \hbox (badness 5756) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for [3263] Underfull \hbox (badness 2913) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower \T1/ptm/m/n/10 , [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [3275] [3276] [3277] [3278] [3279] Underfull \hbox (badness 5036) in paragraph at lines 18341--18350 [][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] [3290] [3291] [3292]) (./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} [3293] Underfull \hbox (badness 1117) 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 \T1/zi4/m/sl/10 response ~ [3294] [3295] [3296] [3297] [3298] [3299] [3300]) (./rpart-pkg.tex Chapter 27. [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./spatial-pkg.tex [3330] Chapter 28. [3331] [3332] [3333] [3334] [3335] [3336] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3337] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349]) (./survival-pkg.tex [3350] Chapter 29. [3351] [3352] [3353] [3354]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3355] [3356] [3357] [3358] [3359] Underfull \vbox (badness 10000) has occurred while \output is active [3360] [3361] [3362] [3363] [3364] [3365] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3366] [3367] [3368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391] [3392] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3393] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3394] [3395] [3396] Underfull \vbox (badness 10000) has occurred while \output is active [3397] Underfull \vbox (badness 10000) has occurred while \output is active [3398] [3399] [3400] [3401] [3402] [3403] [3404] Underfull \vbox (badness 10000) has occurred while \output is active [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] Underfull \hbox (badness 5274) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3418] [3419] [3420] [3421] [3422] [3423] [3424] [3425] [3426] [3427] [3428] Underfull \vbox (badness 2126) has occurred while \output is active [3429] [3430] [3431] Underfull \hbox (badness 1281) in paragraph at lines 5560--5563 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/zi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3432] [3433] [3434] [3435] [3436]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3453] [3454] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3455] [3456] [3457] [3458] [3459] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 , [3460] [3461] [3462] [3463] [3464] Underfull \hbox (badness 1389) in paragraph at lines 7911--7921 []\T1/ptm/m/n/10 One of \T1/zi4/m/sl/10 "none"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "plain"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log" \T1/ptm/m/n/10 (the de-fault), \T 1/zi4/m/sl/10 "log-log" \T1/ptm/m/n/10 or [3465] [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3471] [3472] [3473] [3474] [3475] Underfull \vbox (badness 10000) has occurred while \output is active [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493]) [3494] No file fullrefman.ind. (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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[3] [4] Underfull \hbox (badness 6995) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] [9] [10] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 2671) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1953--1953 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2392--2397 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 5019--5021 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6175--6175 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [91] [92] [93] [94] [95] [96] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6584--6586 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6732--6735 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [99] [100] Underfull \hbox (badness 6063) in paragraph at lines 6914--6920 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- Underfull \hbox (badness 2343) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [101] Underfull \hbox (badness 3568) in paragraph at lines 6976--6983 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] Underfull \hbox (badness 1077) in paragraph at lines 7293--7299 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7293--7299 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7634--7638 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [112] Underfull \hbox (badness 2351) in paragraph at lines 7752--7755 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [113] [114] [115] [116] [117] Underfull \hbox (badness 4479) in paragraph at lines 8078--8088 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 1629) in paragraph at lines 8525--8537 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 1178) in paragraph at lines 9260--9264 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1735) in paragraph at lines 10408--10412 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [150] [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 6396) in paragraph at lines 10847--10855 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 1946) in paragraph at lines 10847--10855 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 4569) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11963--11967 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] Underfull \hbox (badness 2253) in paragraph at lines 13626--13628 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [195] Underfull \hbox (badness 1565) in paragraph at lines 13697--13701 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [196] Underfull \hbox (badness 4927) in paragraph at lines 13741--13743 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4 /m/n/10 fsep = [197] Underfull \hbox (badness 3148) in paragraph at lines 13834--13839 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [198] Underfull \hbox (badness 1466) in paragraph at lines 13881--13884 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [199] Underfull \hbox (badness 10000) in paragraph at lines 14000--14004 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14011--14014 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [200] [201] [202] [203] Underfull \hbox (badness 3965) in paragraph at lines 14301--14305 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] Underfull \hbox (badness 4429) in paragraph at lines 15076--15079 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [216] [217] Underfull \hbox (badness 10000) in paragraph at lines 15198--15202 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 2426) in paragraph at lines 15198--15202 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want Underfull \hbox (badness 2035) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 within [218] [219] [220] [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 2452) in paragraph at lines 15829--15833 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15829--15833 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [227] [228] [229] Underfull \hbox (badness 1092) in paragraph at lines 16002--16007 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [230] [231] [232] Underfull \hbox (badness 6741) in paragraph at lines 16252--16256 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [233] [234] [235] [236] [237] [238] [239] [240] Underfull \vbox (badness 10000) has occurred while \output is active [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] Underfull \hbox (badness 1478) in paragraph at lines 17541--17544 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [251] [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 17796--17798 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1442) in paragraph at lines 18396--18398 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [263] Underfull \hbox (badness 2452) in paragraph at lines 18488--18504 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1248) in paragraph at lines 18907--18910 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [270] [271] [272] [273] Underfull \hbox (badness 4739) in paragraph at lines 19165--19167 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [274] [275] [276] [277] [278] [279] [280] Underfull \hbox (badness 1596) in paragraph at lines 19584--19589 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [281] [282] [283] [284] [285] [286] [287] [288] [289] Underfull \hbox (badness 2469) in paragraph at lines 20188--20193 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and [290] Underfull \hbox (badness 10000) in paragraph at lines 20202--20209 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 10000) in paragraph at lines 20276--20280 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20276--20280 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [291] [292] [293] Underfull \hbox (badness 1014) in paragraph at lines 20446--20451 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 1264) in paragraph at lines 21235--21240 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [305] Underfull \hbox (badness 4441) in paragraph at lines 21264--21267 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] Underfull \hbox (badness 6047) in paragraph at lines 22011--22013 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) == [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] Underfull \hbox (badness 1077) in paragraph at lines 23052--23058 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 2790) in paragraph at lines 23548--23551 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23548--23551 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [340] [341] [342] [343] Underfull \hbox (badness 1194) in paragraph at lines 23830--23833 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [344] [345] Underfull \hbox (badness 2368) in paragraph at lines 24036--24042 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24036--24042 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 24418--24421 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [352] [353] [354] [355] [356] [357] [358] [359] [360] Underfull \hbox (badness 10000) in paragraph at lines 25023--25025 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 1038) in paragraph at lines 25863--25871 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1735) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25872--25875 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [373] Underfull \hbox (badness 2142) in paragraph at lines 26032--26036 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [374] Underfull \hbox (badness 1968) in paragraph at lines 26082--26087 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26383--26386 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26409--26411 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [378] Underfull \hbox (badness 10000) in paragraph at lines 26444--26449 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 2529) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and Underfull \hbox (badness 7203) in paragraph at lines 26462--26465 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26486--26491 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26486--26491 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 10000) in paragraph at lines 27004--27007 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [386] Underfull \hbox (badness 7925) in paragraph at lines 27083--27087 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27083--27087 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27088--27097 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 2726) in paragraph at lines 27809--27812 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] Underfull \hbox (badness 1533) in paragraph at lines 29500--29503 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [423] [424] Underfull \hbox (badness 1163) in paragraph at lines 29663--29674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 10000) in paragraph at lines 31209--31213 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 31209--31213 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [447] Underfull \hbox (badness 6188) in paragraph at lines 31231--31233 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [448] [449] [450] [451] [452] [453] [454] [455] Underfull \hbox (badness 1655) in paragraph at lines 31787--31789 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] Underfull \hbox (badness 2261) in paragraph at lines 32906--32911 []\T1/ptm/m/n/10 If \T1/zi4/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 [472] Underfull \hbox (badness 10000) in paragraph at lines 32933--32939 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 32933--32939 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] Underfull \hbox (badness 1072) in paragraph at lines 36075--36079 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 36080--36084 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', [517] Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 36120--36127 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [518] [519] [520] [521] [522] Underfull \hbox (badness 1142) in paragraph at lines 36473--36479 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1565) in paragraph at lines 37746--37748 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 4967) in paragraph at lines 38345--38350 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [551] [552] Underfull \hbox (badness 1616) in paragraph at lines 38458--38463 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [553] [554] [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1472) in paragraph at lines 38984--38987 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] Underfull \hbox (badness 10000) in paragraph at lines 39898--39902 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [574] [575] [576] [577] Underfull \hbox (badness 10000) in paragraph at lines 40149--40152 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [578] [579] [580] Underfull \hbox (badness 10000) in paragraph at lines 40333--40337 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [581] [582] [583] [584] [585] [586] [587] [588] Underfull \hbox (badness 10000) in paragraph at lines 40946--40949 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [589] [590] [591] [592] [593] Underfull \vbox (badness 10000) has occurred while \output is active [594] [595] [596] [597] [598] [599] [600] [601] Underfull \hbox (badness 1990) in paragraph at lines 41849--41857 []\T1/zi4/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 4846) in paragraph at lines 41849--41857 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [602] [603] [604] [605] [606] [607] [608] Underfull \hbox (badness 1917) in paragraph at lines 42355--42362 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [609] [610] [611] [612] [613] [614] [615] [616] [617] [618] Underfull \hbox (badness 3668) in paragraph at lines 43084--43086 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [619] [620] Underfull \hbox (badness 2401) in paragraph at lines 43212--43216 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [621] [622] [623] Underfull \hbox (badness 2111) in paragraph at lines 43401--43406 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 10000) in paragraph at lines 43422--43427 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 5417) in paragraph at lines 44004--44008 []\T1/zi4/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 [632] Underfull \hbox (badness 10000) in paragraph at lines 44065--44069 []\T1/zi4/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 [633] [634]) (./compiler-pkg.tex Chapter 2. [635] [636] [637] [638]) (./datasets-pkg.tex Chapter 3. [639] [640] [641] [642] [643] [644] Underfull \vbox (badness 1472) has occurred while \output is active [645] [646] [647] [648] [649] [650] [651] [652] [653] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] Overfull \vbox (4.26088pt too high) has occurred while \output is active [676] [677] [678] [679] [680] [681] Overfull \vbox (13.87083pt too high) has occurred while \output is active [682] Underfull \vbox (badness 2376) has occurred while \output is active [683] [684] Overfull \vbox (12.25539pt too high) has occurred while \output is active [685] [686] Overfull \vbox (17.12102pt too high) has occurred while \output is active [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] Overfull \vbox (10.49593pt too high) has occurred while \output is active [698] Overfull \vbox (15.49593pt too high) has occurred while \output is active [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713]) (./grDevices-pkg.tex [714] Chapter 4. [715] [716] [717] [718] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [732] [733] [734] Underfull \hbox (badness 1852) in paragraph at lines 1322--1325 []\T1/zi4/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 [735] [736] [737] Underfull \hbox (badness 1490) in paragraph at lines 1528--1533 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [738] [739] [740] [741] [742] [743] Underfull \hbox (badness 1325) in paragraph at lines 1934--1944 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [744] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [745] [746] [747] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [748] [749] [750] [751] [752] [753] [754] [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [765] [766] [767] [768] [769] [770] Underfull \hbox (badness 10000) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4514--4519 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [781] [782] Underfull \hbox (badness 1067) in paragraph at lines 4668--4675 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [783] [784] [785] [786] Underfull \hbox (badness 1377) in paragraph at lines 4971--4976 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [787] Underfull \hbox (badness 1418) in paragraph at lines 5047--5054 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , [788] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [789] Underfull \hbox (badness 1377) in paragraph at lines 5176--5181 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [790] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [791] [792] Underfull \hbox (badness 2035) in paragraph at lines 5380--5389 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [793] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5448--5455 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [794] [795] Underfull \hbox (badness 1546) in paragraph at lines 5590--5598 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 6125--6128 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [816] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [817] [818] [819] [820] [821] Underfull \hbox (badness 3780) in paragraph at lines 7345--7351 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [822] [823] Underfull \hbox (badness 2680) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [824] [825] [826]) (./graphics-pkg.tex Chapter 5. [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] Underfull \vbox (badness 10000) has occurred while \output is active [842] [843] [844] [845] [846] Underfull \hbox (badness 4634) in paragraph at lines 1349--1352 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] Underfull \hbox (badness 1009) in paragraph at lines 2388--2395 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [863] [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \vbox (badness 10000) has occurred while \output is active [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 3229) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [896] [897] [898] [899] [900] Underfull \hbox (badness 10000) in paragraph at lines 4889--4895 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4889--4895 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [901] Underfull \hbox (badness 10000) in paragraph at lines 5020--5023 [902] Underfull \hbox (badness 10000) in paragraph at lines 5081--5083 [903 ] [904 ] [905] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750 [][] [928 ] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Underfull \hbox (badness 2012) in paragraph at lines 7574--7577 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi nt [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 8834--8836 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [960]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8916 \HeaderA{units}{Graphical Units}{units} [961] [962] [963] [964]) (./grid-pkg.tex Chapter 6. [965] [966] [967] [968] [969] [970] [971] [972] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [973] [974] [975] [976] [977] [978] [979] [980] [981] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] Underfull \vbox (badness 10000) has occurred while \output is active [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1035] [1036] [1037] [1038] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1067] [1068] [1069] [1070]) (./methods-pkg.tex Chapter 7. [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \vbox (badness 10000) has occurred while \output is active [1079] Underfull \vbox (badness 10000) has occurred while \output is active [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1097] [1098] [1099] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1105] [1106] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1107] [1108] [1109] [1110] [1111] [1112] [1113] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1114] [1115] [1116] [1117] [1118] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1119] [1120] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Underfull \vbox (badness 10000) has occurred while \output is active [1139] Underfull \vbox (badness 10000) has occurred while \output is active [1140] [1141] [1142] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1143] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1144] [1145] [1146] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1155] [1156] [1157] [1158] Underfull \vbox (badness 10000) has occurred while \output is active [1159] [1160] [1161]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1162] [1163] [1164]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1165] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1166] [1167] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1201] [1202] [1203] [1204] [1205] [1206] [1207] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1208] [1209] [1210]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1231] [1232]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246]) (./stats-pkg.tex Chapter 10. [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] Underfull \hbox (badness 2503) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 1127) in paragraph at lines 4349--4352 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 3989) in paragraph at lines 4679--4686 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 2556) in paragraph at lines 5315--5318 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5332--5334 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1325] [1326] [1327] [1328] [1329] [1330] Underfull \hbox (badness 2503) in paragraph at lines 5724--5728 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 7081) in paragraph at lines 6518--6521 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6522--6524 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7367--7370 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] Underfull \vbox (badness 10000) has occurred while \output is active [1377] [1378] [1379] [1380] Underfull \hbox (badness 2626) in paragraph at lines 9044--9047 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1381] [1382] Underfull \hbox (badness 2503) in paragraph at lines 9151--9155 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 4518) in paragraph at lines 10461--10466 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 2142) in paragraph at lines 10821--10824 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10840--10843 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1407] Underfull \hbox (badness 1708) in paragraph at lines 10902--10906 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 1694) in paragraph at lines 11298--11301 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1413] [1414] [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 11625--11628 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of Underfull \hbox (badness 1281) in paragraph at lines 11625--11628 \T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia l ap-prox-i-ma-tion may be con-sid-er-ably [1419] [1420]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11779 \aliasA{hat}{influence.measures}{hat} [1421] [1422] Underfull \hbox (badness 1484) in paragraph at lines 11914--11916 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 10000) in paragraph at lines 12507--12509 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit = [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2894) in paragraph at lines 12843--12847 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 13593--13598 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] Underfull \hbox (badness 4518) in paragraph at lines 14245--14250 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1458] [1459] Underfull \hbox (badness 8151) in paragraph at lines 14383--14387 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14390--14392 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] Underfull \hbox (badness 2503) in paragraph at lines 15461--15465 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1477] [1478] [1479] [1480] [1481] [1482] [1483] Underfull \hbox (badness 4621) in paragraph at lines 15973--15979 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/ ptm/m/n/10 and [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] Underfull \vbox (badness 10000) has occurred while \output is active [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1377) in paragraph at lines 18567--18572 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18572--18575 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 18585--18589 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18585--18589 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to [1524] Underfull \hbox (badness 2662) in paragraph at lines 18593--18597 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18818--18818 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18821--18821 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1528] [1529] [1530] [1531] [1532] [1533] Underfull \hbox (badness 1337) in paragraph at lines 19243--19246 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 3049) in paragraph at lines 19739--19743 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1543] [1544] [1545] [1546] Underfull \hbox (badness 1194) in paragraph at lines 19997--20000 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 20372--20375 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1552] Underfull \hbox (badness 3919) in paragraph at lines 20399--20401 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] Underfull \hbox (badness 10000) in paragraph at lines 21476--21482 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Underfull \hbox (badness 1337) in paragraph at lines 22823--22829 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23388--23388 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1599] [1600] [1601] Underfull \hbox (badness 10000) in paragraph at lines 23639--23642 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23639--23642 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 10000) in paragraph at lines 24224--24227 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] = [1611] Underfull \hbox (badness 3690) in paragraph at lines 24276--24280 [][][]\T1/zi4/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 [1612] [1613] [1614] [1615] [1616] [1617] [1618] Underfull \hbox (badness 2165) in paragraph at lines 24753--24758 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1619] [1620] [1621] [1622] Underfull \hbox (badness 1867) in paragraph at lines 24958--24960 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24971--24975 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \vbox (badness 10000) has occurred while \output is active [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \hbox (badness 3514) in paragraph at lines 26510--26515 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] [1646] [1647] [1648] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26744--26744 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1649] Underfull \hbox (badness 3514) in paragraph at lines 26780--26786 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1650] [1651] [1652] Underfull \hbox (badness 3514) in paragraph at lines 26994--26999 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1653] [1654] Underfull \hbox (badness 3514) in paragraph at lines 27081--27086 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1655] Underfull \hbox (badness 3514) in paragraph at lines 27146--27151 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1656] Underfull \hbox (badness 3514) in paragraph at lines 27240--27245 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1657] [1658] Underfull \hbox (badness 6691) in paragraph at lines 27332--27337 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 4024) in paragraph at lines 27862--27865 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 5431) in paragraph at lines 28468--28470 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1676] [1677] [1678] [1679] Underfull \hbox (badness 5431) in paragraph at lines 28678--28681 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1680] [1681] [1682] [1683] [1684] Underfull \hbox (badness 1337) in paragraph at lines 28992--28996 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1685] [1686] [1687] [1688] Underfull \hbox (badness 1616) in paragraph at lines 29294--29297 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1689] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] Underfull \hbox (badness 3557) in paragraph at lines 30424--30428 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4 /m/n/10 interval = [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] [1710] [1711] Underfull \hbox (badness 1337) in paragraph at lines 30788--30792 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719] Underfull \hbox (badness 1337) in paragraph at lines 31315--31319 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728]) (./stats4-pkg.tex Chapter 11. [1729] [1730] [1731] [1732] [1733] [1734]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1735] [1736] [1737]) (./tcltk-pkg.tex [1738] Chapter 12. [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758]) (./tools-pkg.tex Chapter 13. [1759] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1760] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1761] [1762] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1763] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1764] [1765] [1766] [1767] [1768] [1769] [1770] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1776] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1777] [1778] [1779] [1780] [1781] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1782] [1783] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1784] Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1785] [1786] [1787]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1788] [1789] [1790] [1791] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1792] [1793] [1794] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1795] [1796] [1797] [1798] [1799] [1800] [1801] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2837. [1802] [1803] [1804] [1805] Underfull \hbox (badness 1424) in paragraph at lines 3119--3121 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] Underfull \hbox (badness 10000) in paragraph at lines 3823--3825 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1816] [1817] Underfull \hbox (badness 10000) in paragraph at lines 3962--3965 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1818] Underfull \hbox (badness 1137) in paragraph at lines 4064--4066 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1819] [1820] [1821] [1822] [1823] Underfull \hbox (badness 1796) in paragraph at lines 4372--4377 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type == [1824] Underfull \hbox (badness 1838) in paragraph at lines 4446--4452 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4446--4452 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1825] [1826] [1827] Underfull \hbox (badness 2197) in paragraph at lines 4662--4672 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : [1828] Underfull \hbox (badness 1571) in paragraph at lines 4725--4729 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1829] [1830] [1831]) (./utils-pkg.tex [1832] Chapter 14. Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1838] [1839] [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1843] [1844] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1845] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1846] [1847] [1848] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1865] [1866] [1867] [1868] [1869]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.clipboard}) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [1870] [1871] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1872] [1873] [1874] [1875] [1876] [1877] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](...,header = TRUE,sep = [1878] [1879] [1880] [1881] [1882] [1883] [1884] [1885] [1886] [1887] [1888] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1889] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1890] [1891] Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.format}) has been a lready used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] Underfull \hbox (badness 1371) in paragraph at lines 5996--5998 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1919] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1923] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1924] [1925] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1926] [1927] Underfull \hbox (badness 1325) in paragraph at lines 6632--6636 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [1928] Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1929] Underfull \hbox (badness 3219) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6792--6799 [][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [1930] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from [1954] Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [1962] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] Underfull \vbox (badness 5533) has occurred while \output is active [1972] [1973] [1974] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1975] [1976] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1985] Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 11163--11167 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able [1998] Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [1999] [2000] [2001] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2002] [2003] [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2006] [2007] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2008] Underfull \hbox (badness 4779) in paragraph at lines 12237--12239 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a nd Underfull \hbox (badness 1077) in paragraph at lines 12267--12274 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 3780) in paragraph at lines 12668--12672 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 12684--12687 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2015] [2016] [2017] Underfull \hbox (badness 2302) in paragraph at lines 12889--12891 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13185--13190 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13194--13197 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2023] Underfull \vbox (badness 10000) has occurred while \output is active [2024] [2025] [2026] [2027] [2028] Underfull \hbox (badness 2932) in paragraph at lines 13614--13621 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 13614--13621 \T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [2029] [2030] [2031] [2032] Underfull \hbox (badness 6510) in paragraph at lines 13923--13927 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 13930--13933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 13930--13933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 14594--14599 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 14594--14599 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and [2042] Underfull \hbox (badness 1052) in paragraph at lines 14600--14602 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 14659--14662 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] Underfull \hbox (badness 10000) in paragraph at lines 15432--15434 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/zi4/m/sl/10 file = [2055] [2056] [2057]) [2058] [2059] [2060] (./KernSmooth-pkg.tex Chapter 15. [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070]) (./MASS-pkg.tex Chapter 16. [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] Underfull \hbox (badness 7944) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [2108] [2109] [2110] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm /m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative [2111] [2112] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] Underfull \hbox (badness 1117) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2138] Underfull \hbox (badness 1117) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2156] [2157] [2158] [2159] [2160] Underfull \vbox (badness 10000) has occurred while \output is active [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] Underfull \hbox (badness 1117) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2169] Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2170] [2171] [2172] Underfull \hbox (badness 6775) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]) (./Matrix-pkg.tex 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 [2219] 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 [2220] [2221] [2222] [2223] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2224] [2225] Underfull \hbox (badness 2418) in paragraph at lines 597--600 []\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2226] [2227] [2228] [2229] [2230] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a-lently, \T1/zi4/m/sl/10 to = [2231] [2232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} Underfull \hbox (badness 1117) in paragraph at lines 1189--1195 \T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t he same al-go-rithm [2233pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol ,dsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works via] [2234] [2235] Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2236] [2237] Underfull \hbox (badness 1097) in paragraph at lines 1560--1563 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2238]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2239] [2240] [2241] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2242] [2243] [2244] [2245] [2246] Underfull \hbox (badness 1360) in paragraph at lines 2295--2299 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via [2247] [2248] [2249] [2250] Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble [2251] [2252] Underfull \hbox (badness 6842) in paragraph at lines 2700--2703 []\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2253] Underfull \hbox (badness 10000) in paragraph at lines 2986--2990 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro up meth-ods re-turn a [2254] [2255] [2256] Underfull \hbox (badness 1173) in paragraph at lines 3196--3198 []\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2257] [2258] Underfull \hbox (badness 1354) in paragraph at lines 3442--3445 []\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex -plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in -her-it-ing from [2259] [2260] [2261] [2262] [2263] Underfull \hbox (badness 6188) in paragraph at lines 3852--3855 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = Underfull \hbox (badness 5147) in paragraph at lines 3855--3858 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = [2264] [2265] Underfull \hbox (badness 2318) in paragraph at lines 3969--3973 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2266] [2267] Underfull \hbox (badness 5245) in paragraph at lines 4105--4109 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1 0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x) [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (3.77782pt too wide) in paragraph at lines 4527--4527 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (48.77782pt too wide) in paragraph at lines 4530--4530 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2274] [2275] Underfull \hbox (badness 1931) in paragraph at lines 4762--4764 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2276] [2277] [2278] [2279] [2280] Underfull \hbox (badness 1005) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA \T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1655) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4 /m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2281] Overfull \hbox (42.75635pt too wide) in paragraph at lines 5134--5134 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2282] Underfull \hbox (badness 3229) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2283] Underfull \hbox (badness 4995) in paragraph at lines 5282--5285 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 5292--5295 []\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional [2284] [2285] [2286] [2287] [2288] Underfull \hbox (badness 1014) in paragraph at lines 5669--5672 []\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10 is a tri-an-gu-lar ma-trix. Anal-o-gously, [2289] [2290] [2291] [2292] Underfull \hbox (badness 10000) in paragraph at lines 5984--5987 []\T1/zi4/m/sl/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 [2293] Underfull \hbox (badness 2478) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2294] Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2295] Underfull \hbox (badness 10000) in paragraph at lines 6296--6299 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2296] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2297] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2298] Underfull \hbox (badness 2050) in paragraph at lines 6545--6548 []\T1/zi4/m/sl/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 [2299] [2300] [2301] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2302] Underfull \hbox (badness 6268) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2303]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1527) in paragraph at lines 6961--6963 []\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \ T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 6966--6969 []\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 [2304]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2305pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod.Rdash.methods}) has be en already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 ] [2306] Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 1448) in paragraph at lines 7426--7431 \T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 1264) in paragraph at lines 7441--7442 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures, see [2307] [2308] Underfull \hbox (badness 1430) in paragraph at lines 7585--7590 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2309] Underfull \hbox (badness 10000) in paragraph at lines 7656--7659 []\T1/zi4/m/sl/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 [2310] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X [2311] [2312] Underfull \vbox (badness 10000) has occurred while \output is active [2313] Underfull \hbox (badness 2478) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2314] [2315] Underfull \hbox (badness 5924) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim-ple meth-ods [2316]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2317] [2318] Underfull \hbox (badness 10000) in paragraph at lines 8427--8430 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2319] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2320] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2321] Underfull \vbox (badness 10000) has occurred while \output is active [2322] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 8724--8727 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low [2323] [2324] [2325] [2326]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2327] [2328] [2329] [2330]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.rcond}) has been already u sed, duplicate ignored \relax l.9252 ... the Reciprocal Condition Number}{rcond} [2331] [2332] [2333] [2334] Underfull \hbox (badness 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1852) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][]( nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 --- Underfull \hbox (badness 2343) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.solve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} [2339] Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse = [2340] Underfull \hbox (badness 4403) in paragraph at lines 10053--10056 []\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing \T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame [2341] Underfull \hbox (badness 10000) in paragraph at lines 10159--10162 []\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co -er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] Underfull \hbox (badness 10000) in paragraph at lines 10758--10766 []\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 10758--10766 \T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [2350]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2351] [2352] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2353] [2354] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2355] Underfull \vbox (badness 10000) has occurred while \output is active [2356] [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/ sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be [2359] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2360] [2361] Underfull \hbox (badness 1831) in paragraph at lines 11740--11746 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2362] Underfull \hbox (badness 1902) in paragraph at lines 11775--11779 []\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a nd other [2363] [2364] [2365] [2366] [2367] [2368] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2369] [2370] [2371]) (./boot-pkg.tex [2372] Chapter 18. [2373] [2374] [2375] [2376] [2377] [2378] [2379] [2380] [2381] [2382] Underfull \hbox (badness 1297) in paragraph at lines 797--807 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour [2383] 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. [2384] Underfull \vbox (badness 10000) has occurred while \output is active [2385] [2386] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 1859) in paragraph at lines 1066--1070 \T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will [2387] 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 [2388] [2389] [2390] [2391] 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- [2392] [2393] [2394] [2395] [2396] [2397] Underfull \hbox (badness 1005) in paragraph at lines 1797--1804 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2398] [2399] Underfull \vbox (badness 10000) has occurred while \output is active [2400] Underfull \hbox (badness 7379) 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. [2401] [2402] [2403] [2404] 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 [2405] 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. [2406] [2407] Underfull \hbox (badness 2970) 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/zi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] 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 [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] 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 [2442] [2443] [2444] [2445] 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 [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] [2455] [2456] Underfull \hbox (badness 4954) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475]) (./class-pkg.tex [2476] Chapter 19. [2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492]) (./cluster-pkg.tex Chapter 20. [2493] [2494] [2495] [2496] [2497] Underfull \vbox (badness 7777) has occurred while \output is active [2498] [2499] [2500] [2501] [2502] Underfull \hbox (badness 4144) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2506] [2507] Underfull \hbox (badness 10000) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2508] [2509] [2510] Underfull \hbox (badness 6110) in paragraph at lines 1189--1193 []\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2511] [2512] [2513] Underfull \hbox (badness 10000) in paragraph at lines 1458--1461 [2514] [2515] Underfull \hbox (badness 2503) in paragraph at lines 1570--1573 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 2161--2164 Underfull \hbox (badness 10000) in paragraph at lines 2175--2181 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2524] [2525] [2526] [2527] Underfull \hbox (badness 6675) in paragraph at lines 2410--2412 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2528] [2529] [2530] [2531] [2532] [2533] [2534] Underfull \hbox (badness 2980) in paragraph at lines 2901--2905 [][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2535] [2536] [2537] [2538] [2539] Underfull \hbox (badness 1142) in paragraph at lines 3242--3245 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2540] [2541] Underfull \hbox (badness 1142) in paragraph at lines 3361--3364 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2542] [2543] [2544] [2545] Underfull \hbox (badness 2582) in paragraph at lines 3584--3589 [][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2546] Underfull \hbox (badness 3209) in paragraph at lines 3646--3651 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi 4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which Underfull \hbox (badness 8019) in paragraph at lines 3646--3651 \T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/ m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx [2547] [2548] [2549] [2550] Underfull \hbox (badness 10000) in paragraph at lines 3938--3940 []\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2551] [2552] [2553] [2554] Underfull \hbox (badness 2626) in paragraph at lines 4162--4167 []\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col = [2555] Underfull \hbox (badness 1383) in paragraph at lines 4240--4245 []\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2556] [2557] [2558] [2559] [2560] [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 4668--4670 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2563]) (./codetools-pkg.tex [2564] Chapter 21. [2565] [2566] [2567] [2568] [2569]) (./foreign-pkg.tex [2570] Chapter 22. [2571] [2572] [2573] [2574] [2575] [2576] [2577] [2578] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de -fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to [2579] Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 813--814 [2583] [2584] [2585] [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2590] [2591]) (./lattice-pkg.tex [2592] Chapter 23. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2609] Underfull \vbox (badness 4416) has occurred while \output is active [2610] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2611] [2612] [2613] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to 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 [2614] [2615] [2616] [2617] [2618] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, the value of [2619] [2620] [2621] [2622] [2623] [2624] [2625] [2626] [2627] [2628] Underfull \hbox (badness 2781) in paragraph at lines 2848--2850 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2629] Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2630] [2631] [2632] [2633] [2634] [2635] [2636]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.parallel}) has been already used, duplic ate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} [2637] [2638] [2639] [2640] [2641] [2642] [2643] Underfull \hbox (badness 5696) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2644] [2645] Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2646] [2647] [2648] Underfull \hbox (badness 3492) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2649] [2650] [2651] [2652] [2653] [2654] [2655] [2656] [2657] [2658] Underfull \hbox (badness 6157) in paragraph at lines 5035--5038 []\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2659] [2660] [2661] [2662] [2663] [2664] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5486--5489 \T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2665] [2666] [2667] [2668] [2669] Underfull \hbox (badness 4805) in paragraph at lines 5846--5850 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5857--5864 \T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5857--5864 [][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2670] [2671] [2672] [2673] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6157--6162 \T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2674] [2675] Underfull \hbox (badness 2310) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 3168) in paragraph at lines 7055--7059 \T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U se [2687] [2688] [2689] [2690] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2691] [2692] Underfull \hbox (badness 3333) in paragraph at lines 7498--7500 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2693] [2694] [2695] Underfull \vbox (badness 10000) has occurred while \output is active [2696] [2697] [2698] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2707] Underfull \hbox (badness 1092) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2708] [2709] Underfull \hbox (badness 3895) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2710] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2711] [2712] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 8876--8879 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2713] [2714] [2715] [2716] Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4 /m/sl/10 left,right,left.name,right.name,condition [2717] [2718] [2719] [2720] [2721] [2722] [2723] Underfull \hbox (badness 2310) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2724] [2725] [2726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2727] [2728] [2729] Underfull \hbox (badness 4144) in paragraph at lines 10077--10080 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10077--10080 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2730] [2731]) (./mgcv-pkg.tex [2732] Chapter 24. [2733] [2734] [2735] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2736] [2737] [2738] [2739] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/ n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 365--372 [][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][] []\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][] \T1/ptm/m/n/10 , [2740] [2741] [2742] [2743] [2744] [2745] [2746] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2747] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2748] Underfull \vbox (badness 10000) has occurred while \output is active [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] Underfull \hbox (badness 1142) in paragraph at lines 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2772] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2773] [2774] [2775] [2776] [2777] Underfull \vbox (badness 10000) has occurred while \output is active [2778] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \vbox (badness 10000) has occurred while \output is active [2780] [2781] [2782] [2783] [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2794] [2795] Underfull \vbox (badness 10000) has occurred while \output is active [2796] [2797] [2798] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2799] [2800] [2801] [2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2811] Underfull \hbox (badness 1231) in paragraph at lines 4692--4694 []\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with [2812] [2813] [2814] Underfull \vbox (badness 10000) has occurred while \output is active [2815] [2816] [2817] Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 10000) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(... ,fit=FALSE) \T1/ptm/m/n/10 or [2825] [2826] Underfull \vbox (badness 10000) has occurred while \output is active [2827] [2828] [2829] [2830] [2831] [2832] [2833] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2834] [2835] [2836] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] Underfull \hbox (badness 1087) in paragraph at lines 6326--6327 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas e, and if [2841] [2842] [2843] Underfull \vbox (badness 10000) has occurred while \output is active [2844] Underfull \vbox (badness 10000) has occurred while \output is active [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] [2867] Underfull \hbox (badness 6001) in paragraph at lines 7912--7914 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] Underfull \hbox (badness 1038) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2880] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] Underfull \hbox (badness 1852) in paragraph at lines 9387--9390 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2892] [2893] [2894] Underfull \hbox (badness 1852) in paragraph at lines 9551--9554 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2895] [2896] Underfull \vbox (badness 10000) has occurred while \output is active [2897] [2898] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2899] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2900] [2901] [2902] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2903] [2904] [2905] [2906] Underfull \hbox (badness 4792) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/ 10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m /n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2907] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1 0 "deviance"\T1/ptm/m/n/10 , [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [2919] [2920] Underfull \hbox (badness 1320) in paragraph at lines 11084--11089 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T 1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If ma- [2921] [2922] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2923] Underfull \hbox (badness 1762) in paragraph at lines 11279--11291 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Underfull \hbox (badness 7667) in paragraph at lines 11491--11497 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2934] [2935] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2936] [2937] Underfull \hbox (badness 1436) in paragraph at lines 12074--12081 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2938] [2939] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 12754--12760 \T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T 1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] [2955] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2956] [2957] [2958] [2959] Underfull \hbox (badness 3895) in paragraph at lines 13358--13361 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2960] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2961] [2962] [2963] [2964] Underfull \hbox (badness 1371) in paragraph at lines 13620--13626 []\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de fined.smooth[][][]\T1/ptm/m/n/10 , Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4 /m/sl/10 factor.smooth.interaction[][][] [2965] [2966] [2967] [2968] Underfull \hbox (badness 2326) in paragraph at lines 13865--13872 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2969] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978] [2979] [2980] Underfull \vbox (badness 10000) has occurred while \output is active [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] Underfull \hbox (badness 1796) in paragraph at lines 15594--15597 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2997] [2998] [2999] [3000] [3001] [3002]) (./nlme-pkg.tex Chapter 25. [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 2875) in paragraph at lines 1994--2000 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 2256--2262 [][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 1067) in paragraph at lines 4414--4419 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3070] [3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [3082] [3083] [3084] [3085] [3086] [3087] [3088] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [3089] [3090] [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 10000) in paragraph at lines 5973--5978 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [3096] [3097] [3098] [3099] Underfull \hbox (badness 1490) in paragraph at lines 6243--6254 [][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [3100] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3101] [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3107] [3108] [3109] [3110] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [3111] [3112] [3113] [3114] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3134]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig ma}) has been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3135] [3136] [3137] [3138] Underfull \hbox (badness 10000) in paragraph at lines 8802--8809 [][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [3147] [3148] [3149] [3150] [3151]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3164] [3165] Underfull \hbox (badness 1490) in paragraph at lines 10597--10603 [][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1286) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] Underfull \hbox (badness 1067) in paragraph at lines 15888--15893 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3244] [3245] [3246] [3247] Underfull \hbox (badness 1448) in paragraph at lines 16131--16140 \T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3248] [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3258] [3259] [3260] [3261] [3262] Underfull \hbox (badness 8056) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural Underfull \hbox (badness 5756) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for [3263] Underfull \hbox (badness 2913) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower \T1/ptm/m/n/10 , [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [3275] [3276] [3277] [3278] [3279] Underfull \hbox (badness 5036) in paragraph at lines 18341--18350 [][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] [3290] [3291] [3292]) (./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} [3293] Underfull \hbox (badness 1117) 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 \T1/zi4/m/sl/10 response ~ [3294] [3295] [3296] [3297] [3298] [3299] [3300]) (./rpart-pkg.tex Chapter 27. [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./spatial-pkg.tex [3330] Chapter 28. [3331] [3332] [3333] [3334] [3335] [3336] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3337] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349]) (./survival-pkg.tex [3350] Chapter 29. [3351] [3352] [3353] [3354]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3355] [3356] [3357] [3358] [3359] Underfull \vbox (badness 10000) has occurred while \output is active [3360] [3361] [3362] [3363] [3364] [3365] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3366] [3367] [3368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391] [3392] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3393] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3394] [3395] [3396] Underfull \vbox (badness 10000) has occurred while \output is active [3397] Underfull \vbox (badness 10000) has occurred while \output is active [3398] [3399] [3400] [3401] [3402] [3403] [3404] Underfull \vbox (badness 10000) has occurred while \output is active [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] Underfull \hbox (badness 5274) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3418] [3419] [3420] [3421] [3422] [3423] [3424] [3425] [3426] [3427] [3428] Underfull \vbox (badness 2126) has occurred while \output is active [3429] [3430] [3431] Underfull \hbox (badness 1281) in paragraph at lines 5560--5563 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/zi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3432] [3433] [3434] [3435] [3436]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3453] [3454] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3455] [3456] [3457] [3458] [3459] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 , [3460] [3461] [3462] [3463] [3464] Underfull \hbox (badness 1389) in paragraph at lines 7911--7921 []\T1/ptm/m/n/10 One of \T1/zi4/m/sl/10 "none"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "plain"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log" \T1/ptm/m/n/10 (the de-fault), \T 1/zi4/m/sl/10 "log-log" \T1/ptm/m/n/10 or [3465] [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3471] [3472] [3473] [3474] [3475] Underfull \vbox (badness 10000) has occurred while \output is active [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493]) [3494] (./fullrefman.ind [3495] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504] [3505] [3506] [3507] [3508] [3509] [3510] [3511] [3512] [3513] [3514] [3515] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2229--2231 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [3516] [3517] [3518] [3519] [3520] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2795--2797 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [3521] [3522] [3523] [3524] [3525] [3526] [3527] [3528] [3529] Overfull \hbox (20.8567pt too wide) in paragraph at lines 3939--3941 []\T1/zi4/m/it/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 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lines 4586--4588 []\T1/zi4/m/it/10 %&%,nsparseMatrix,nsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 4590--4592 []\T1/zi4/m/it/10 %&%,sparseMatrix,diagonalMatrix-method [3536] Overfull \hbox (15.01662pt too wide) in paragraph at lines 4771--4773 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3537] Overfull \hbox (20.8567pt too wide) in paragraph at lines 4932--4934 []\T1/zi4/m/it/10 all.equal,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 4934--4936 []\T1/zi4/m/it/10 all.equal,sparseMatrix,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 4938--4940 []\T1/zi4/m/it/10 all.equal,sparseVector,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 4940--4942 []\T1/zi4/m/it/10 all.equal,sparseVector,sparseVector-method [3538] Overfull \hbox (10.8567pt too wide) in paragraph at lines 5198--5200 []\T1/zi4/m/it/10 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paragraph at lines 7412--7414 []\T1/zi4/m/it/10 coerce,CsparseMatrix,symmetricMatrix-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 7414--7416 []\T1/zi4/m/it/10 coerce,CsparseMatrix,TsparseMatrix-method [3550] Overfull \hbox (5.8567pt too wide) in paragraph at lines 7430--7432 []\T1/zi4/m/it/10 coerce,ddiMatrix,symmetricMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 7432--7434 []\T1/zi4/m/it/10 coerce,ddiMatrix,triangularMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 7436--7438 []\T1/zi4/m/it/10 coerce,denseMatrix,CsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 7438--7440 []\T1/zi4/m/it/10 coerce,denseMatrix,generalMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 7440--7442 []\T1/zi4/m/it/10 coerce,denseMatrix,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 7442--7444 []\T1/zi4/m/it/10 coerce,denseMatrix,sparseMatrix-method Overfull \hbox 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coerce,diagonalMatrix,nsparseMatrix-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 7518--7520 []\T1/zi4/m/it/10 coerce,diagonalMatrix,sparseVector-method [3551] Overfull \hbox (0.8567pt too wide) in paragraph at lines 7566--7568 []\T1/zi4/m/it/10 coerce,dsparseMatrix,matrix.csr-method [3552] Overfull \hbox (5.8567pt too wide) in paragraph at lines 7718--7720 []\T1/zi4/m/it/10 coerce,ldiMatrix,symmetricMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 7720--7722 []\T1/zi4/m/it/10 coerce,ldiMatrix,triangularMatrix-method [3553] Overfull \hbox (10.8567pt too wide) in paragraph at lines 7752--7754 []\T1/zi4/m/it/10 coerce,lgeMatrix,triangularMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 7766--7768 []\T1/zi4/m/it/10 coerce,lgTMatrix,symmetricMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 7768--7770 []\T1/zi4/m/it/10 coerce,lgTMatrix,triangularMatrix-method Overfull \hbox (15.8567pt too wide) in 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[3] [4] Underfull \hbox (badness 6995) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [5] [6] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [7] [8] [9] [10] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 2671) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1953--1953 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2392--2397 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 5019--5021 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6175--6175 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [91] [92] [93] [94] [95] [96] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6584--6586 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6732--6735 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [99] [100] Underfull \hbox (badness 6063) in paragraph at lines 6914--6920 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- Underfull \hbox (badness 2343) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6914--6920 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [101] Underfull \hbox (badness 3568) in paragraph at lines 6976--6983 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] Underfull \hbox (badness 1077) in paragraph at lines 7293--7299 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7293--7299 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7634--7638 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [112] Underfull \hbox (badness 2351) in paragraph at lines 7752--7755 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [113] [114] [115] [116] [117] Underfull \hbox (badness 4479) in paragraph at lines 8078--8088 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 1629) in paragraph at lines 8525--8537 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8525--8537 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 1178) in paragraph at lines 9260--9264 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1735) in paragraph at lines 10408--10412 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [150] [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 6396) in paragraph at lines 10847--10855 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 1946) in paragraph at lines 10847--10855 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 4569) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11963--11967 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] Underfull \hbox (badness 2253) in paragraph at lines 13626--13628 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [195] Underfull \hbox (badness 1565) in paragraph at lines 13697--13701 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [196] Underfull \hbox (badness 4927) in paragraph at lines 13741--13743 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4 /m/n/10 fsep = [197] Underfull \hbox (badness 3148) in paragraph at lines 13834--13839 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [198] Underfull \hbox (badness 1466) in paragraph at lines 13881--13884 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [199] Underfull \hbox (badness 10000) in paragraph at lines 14000--14004 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14011--14014 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [200] [201] [202] [203] Underfull \hbox (badness 3965) in paragraph at lines 14301--14305 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] Underfull \hbox (badness 4429) in paragraph at lines 15076--15079 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [216] [217] Underfull \hbox (badness 10000) in paragraph at lines 15198--15202 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 2426) in paragraph at lines 15198--15202 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want Underfull \hbox (badness 2035) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 within [218] [219] [220] [221] [222] [223] [224] [225] [226] Underfull \hbox (badness 2452) in paragraph at lines 15829--15833 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15829--15833 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [227] [228] [229] Underfull \hbox (badness 1092) in paragraph at lines 16002--16007 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [230] [231] [232] Underfull \hbox (badness 6741) in paragraph at lines 16252--16256 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [233] [234] [235] [236] [237] [238] [239] [240] Underfull \vbox (badness 10000) has occurred while \output is active [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] Underfull \hbox (badness 1478) in paragraph at lines 17541--17544 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [251] [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 17796--17798 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1442) in paragraph at lines 18396--18398 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [263] Underfull \hbox (badness 2452) in paragraph at lines 18488--18504 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1248) in paragraph at lines 18907--18910 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [270] [271] [272] [273] Underfull \hbox (badness 4739) in paragraph at lines 19165--19167 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [274] [275] [276] [277] [278] [279] [280] Underfull \hbox (badness 1596) in paragraph at lines 19584--19589 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [281] [282] [283] [284] [285] [286] [287] [288] [289] Underfull \hbox (badness 2469) in paragraph at lines 20188--20193 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and [290] Underfull \hbox (badness 10000) in paragraph at lines 20202--20209 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 10000) in paragraph at lines 20276--20280 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20276--20280 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [291] [292] [293] Underfull \hbox (badness 1014) in paragraph at lines 20446--20451 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 1264) in paragraph at lines 21235--21240 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [305] Underfull \hbox (badness 4441) in paragraph at lines 21264--21267 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] Underfull \hbox (badness 6047) in paragraph at lines 22011--22013 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) == [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] Underfull \hbox (badness 1077) in paragraph at lines 23052--23058 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 2790) in paragraph at lines 23548--23551 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23548--23551 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [340] [341] [342] [343] Underfull \hbox (badness 1194) in paragraph at lines 23830--23833 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [344] [345] Underfull \hbox (badness 2368) in paragraph at lines 24036--24042 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24036--24042 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 24418--24421 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [352] [353] [354] [355] [356] [357] [358] [359] [360] Underfull \hbox (badness 10000) in paragraph at lines 25023--25025 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 1038) in paragraph at lines 25863--25871 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1735) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25863--25871 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25872--25875 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [373] Underfull \hbox (badness 2142) in paragraph at lines 26032--26036 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [374] Underfull \hbox (badness 1968) in paragraph at lines 26082--26087 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26370--26376 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26383--26386 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26409--26411 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [378] Underfull \hbox (badness 10000) in paragraph at lines 26444--26449 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 2529) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26450--26461 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and Underfull \hbox (badness 7203) in paragraph at lines 26462--26465 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26486--26491 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26486--26491 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 10000) in paragraph at lines 27004--27007 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [386] Underfull \hbox (badness 7925) in paragraph at lines 27083--27087 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27083--27087 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27088--27097 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 2726) in paragraph at lines 27809--27812 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] Underfull \hbox (badness 1533) in paragraph at lines 29500--29503 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [423] [424] Underfull \hbox (badness 1163) in paragraph at lines 29663--29674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 10000) in paragraph at lines 31209--31213 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 31209--31213 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [447] Underfull \hbox (badness 6188) in paragraph at lines 31231--31233 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [448] [449] [450] [451] [452] [453] [454] [455] Underfull \hbox (badness 1655) in paragraph at lines 31787--31789 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] Underfull \hbox (badness 2261) in paragraph at lines 32906--32911 []\T1/ptm/m/n/10 If \T1/zi4/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 [472] Underfull \hbox (badness 10000) in paragraph at lines 32933--32939 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 32933--32939 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] Underfull \hbox (badness 1072) in paragraph at lines 36075--36079 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 36080--36084 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', [517] Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 36108--36114 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 36120--36127 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 36120--36127 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [518] [519] [520] [521] [522] Underfull \hbox (badness 1142) in paragraph at lines 36473--36479 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1565) in paragraph at lines 37746--37748 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 4967) in paragraph at lines 38345--38350 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [551] [552] Underfull \hbox (badness 1616) in paragraph at lines 38458--38463 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [553] [554] [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1472) in paragraph at lines 38984--38987 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] Underfull \hbox (badness 10000) in paragraph at lines 39898--39902 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [574] [575] [576] [577] Underfull \hbox (badness 10000) in paragraph at lines 40149--40152 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [578] [579] [580] Underfull \hbox (badness 10000) in paragraph at lines 40333--40337 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [581] [582] [583] [584] [585] [586] [587] [588] Underfull \hbox (badness 10000) in paragraph at lines 40946--40949 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [589] [590] [591] [592] [593] Underfull \vbox (badness 10000) has occurred while \output is active [594] [595] [596] [597] [598] [599] [600] [601] Underfull \hbox (badness 1990) in paragraph at lines 41849--41857 []\T1/zi4/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 4846) in paragraph at lines 41849--41857 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [602] [603] [604] [605] [606] [607] [608] Underfull \hbox (badness 1917) in paragraph at lines 42355--42362 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [609] [610] [611] [612] [613] [614] [615] [616] [617] [618] Underfull \hbox (badness 3668) in paragraph at lines 43084--43086 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [619] [620] Underfull \hbox (badness 2401) in paragraph at lines 43212--43216 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [621] [622] [623] Underfull \hbox (badness 2111) in paragraph at lines 43401--43406 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 10000) in paragraph at lines 43422--43427 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 5417) in paragraph at lines 44004--44008 []\T1/zi4/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 [632] Underfull \hbox (badness 10000) in paragraph at lines 44065--44069 []\T1/zi4/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 [633] [634]) (./compiler-pkg.tex Chapter 2. [635] [636] [637] [638]) (./datasets-pkg.tex Chapter 3. [639] [640] [641] [642] [643] [644] Underfull \vbox (badness 1472) has occurred while \output is active [645] [646] [647] [648] [649] [650] [651] [652] [653] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] Overfull \vbox (4.26088pt too high) has occurred while \output is active [676] [677] [678] [679] [680] [681] Overfull \vbox (13.87083pt too high) has occurred while \output is active [682] Underfull \vbox (badness 2376) has occurred while \output is active [683] [684] Overfull \vbox (12.25539pt too high) has occurred while \output is active [685] [686] Overfull \vbox (17.12102pt too high) has occurred while \output is active [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] Overfull \vbox (10.49593pt too high) has occurred while \output is active [698] Overfull \vbox (15.49593pt too high) has occurred while \output is active [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713]) (./grDevices-pkg.tex [714] Chapter 4. [715] [716] [717] [718] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [732] [733] [734] Underfull \hbox (badness 1852) in paragraph at lines 1322--1325 []\T1/zi4/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 [735] [736] [737] Underfull \hbox (badness 1490) in paragraph at lines 1528--1533 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [738] [739] [740] [741] [742] [743] Underfull \hbox (badness 1325) in paragraph at lines 1934--1944 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [744] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [745] [746] [747] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [748] [749] [750] [751] [752] [753] [754] [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [765] [766] [767] [768] [769] [770] Underfull \hbox (badness 10000) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4514--4519 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [781] [782] Underfull \hbox (badness 1067) in paragraph at lines 4668--4675 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [783] [784] [785] [786] Underfull \hbox (badness 1377) in paragraph at lines 4971--4976 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [787] Underfull \hbox (badness 1418) in paragraph at lines 5047--5054 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , [788] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [789] Underfull \hbox (badness 1377) in paragraph at lines 5176--5181 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [790] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [791] [792] Underfull \hbox (badness 2035) in paragraph at lines 5380--5389 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5380--5389 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [793] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5448--5455 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [794] [795] Underfull \hbox (badness 1546) in paragraph at lines 5590--5598 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 6125--6128 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [816] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [817] [818] [819] [820] [821] Underfull \hbox (badness 3780) in paragraph at lines 7345--7351 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [822] [823] Underfull \hbox (badness 2680) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [824] [825] [826]) (./graphics-pkg.tex Chapter 5. [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] Underfull \vbox (badness 10000) has occurred while \output is active [842] [843] [844] [845] [846] Underfull \hbox (badness 4634) in paragraph at lines 1349--1352 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] Underfull \hbox (badness 1009) in paragraph at lines 2388--2395 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [863] [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \vbox (badness 10000) has occurred while \output is active [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] Underfull \hbox (badness 3229) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [896] [897] [898] [899] [900] Underfull \hbox (badness 10000) in paragraph at lines 4889--4895 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4889--4895 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [901] Underfull \hbox (badness 10000) in paragraph at lines 5020--5023 [902] Underfull \hbox (badness 10000) in paragraph at lines 5081--5083 [903 ] [904 ] [905] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6749--6750 [][] [928 ] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Underfull \hbox (badness 2012) in paragraph at lines 7574--7577 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi nt [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 8834--8836 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [960]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8916 \HeaderA{units}{Graphical Units}{units} [961] [962] [963] [964]) (./grid-pkg.tex Chapter 6. [965] [966] [967] [968] [969] [970] [971] [972] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [973] [974] [975] [976] [977] [978] [979] [980] [981] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] Underfull \vbox (badness 10000) has occurred while \output is active [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1035] [1036] [1037] [1038] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1067] [1068] [1069] [1070]) (./methods-pkg.tex Chapter 7. [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \vbox (badness 10000) has occurred while \output is active [1079] Underfull \vbox (badness 10000) has occurred while \output is active [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1097] [1098] [1099] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1105] [1106] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1107] [1108] [1109] [1110] [1111] [1112] [1113] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1114] [1115] [1116] [1117] [1118] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1119] [1120] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Underfull \vbox (badness 10000) has occurred while \output is active [1139] Underfull \vbox (badness 10000) has occurred while \output is active [1140] [1141] [1142] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1143] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1144] [1145] [1146] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1155] [1156] [1157] [1158] Underfull \vbox (badness 10000) has occurred while \output is active [1159] [1160] [1161]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1162] [1163] [1164]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1165] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1166] [1167] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1201] [1202] [1203] [1204] [1205] [1206] [1207] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1208] [1209] [1210]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1231] [1232]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246]) (./stats-pkg.tex Chapter 10. [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] Underfull \hbox (badness 2503) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 1127) in paragraph at lines 4349--4352 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 3989) in paragraph at lines 4679--4686 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 2556) in paragraph at lines 5315--5318 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5332--5334 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1325] [1326] [1327] [1328] [1329] [1330] Underfull \hbox (badness 2503) in paragraph at lines 5724--5728 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 7081) in paragraph at lines 6518--6521 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6522--6524 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7367--7370 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] Underfull \vbox (badness 10000) has occurred while \output is active [1377] [1378] [1379] [1380] Underfull \hbox (badness 2626) in paragraph at lines 9044--9047 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1381] [1382] Underfull \hbox (badness 2503) in paragraph at lines 9151--9155 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 4518) in paragraph at lines 10461--10466 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 2142) in paragraph at lines 10821--10824 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10840--10843 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1407] Underfull \hbox (badness 1708) in paragraph at lines 10902--10906 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 1694) in paragraph at lines 11298--11301 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1413] [1414] [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 11625--11628 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of Underfull \hbox (badness 1281) in paragraph at lines 11625--11628 \T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia l ap-prox-i-ma-tion may be con-sid-er-ably [1419] [1420]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11779 \aliasA{hat}{influence.measures}{hat} [1421] [1422] Underfull \hbox (badness 1484) in paragraph at lines 11914--11916 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] Underfull \hbox (badness 10000) in paragraph at lines 12507--12509 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit = [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2894) in paragraph at lines 12843--12847 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 13593--13598 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] Underfull \hbox (badness 4518) in paragraph at lines 14245--14250 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1458] [1459] Underfull \hbox (badness 8151) in paragraph at lines 14383--14387 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14390--14392 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] Underfull \hbox (badness 2503) in paragraph at lines 15461--15465 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1477] [1478] [1479] [1480] [1481] [1482] [1483] Underfull \hbox (badness 4621) in paragraph at lines 15973--15979 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/ ptm/m/n/10 and [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] Underfull \vbox (badness 10000) has occurred while \output is active [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1377) in paragraph at lines 18567--18572 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18572--18575 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 18585--18589 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18585--18589 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to [1524] Underfull \hbox (badness 2662) in paragraph at lines 18593--18597 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18818--18818 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18821--18821 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1528] [1529] [1530] [1531] [1532] [1533] Underfull \hbox (badness 1337) in paragraph at lines 19243--19246 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 3049) in paragraph at lines 19739--19743 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1543] [1544] [1545] [1546] Underfull \hbox (badness 1194) in paragraph at lines 19997--20000 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 20372--20375 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1552] Underfull \hbox (badness 3919) in paragraph at lines 20399--20401 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] Underfull \hbox (badness 10000) in paragraph at lines 21476--21482 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Underfull \hbox (badness 1337) in paragraph at lines 22823--22829 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23388--23388 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1599] [1600] [1601] Underfull \hbox (badness 10000) in paragraph at lines 23639--23642 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23639--23642 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 10000) in paragraph at lines 24224--24227 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] = [1611] Underfull \hbox (badness 3690) in paragraph at lines 24276--24280 [][][]\T1/zi4/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 [1612] [1613] [1614] [1615] [1616] [1617] [1618] Underfull \hbox (badness 2165) in paragraph at lines 24753--24758 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1619] [1620] [1621] [1622] Underfull \hbox (badness 1867) in paragraph at lines 24958--24960 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24971--24975 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \vbox (badness 10000) has occurred while \output is active [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \hbox (badness 3514) in paragraph at lines 26510--26515 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] [1646] [1647] [1648] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26744--26744 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1649] Underfull \hbox (badness 3514) in paragraph at lines 26780--26786 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1650] [1651] [1652] Underfull \hbox (badness 3514) in paragraph at lines 26994--26999 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1653] [1654] Underfull \hbox (badness 3514) in paragraph at lines 27081--27086 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1655] Underfull \hbox (badness 3514) in paragraph at lines 27146--27151 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1656] Underfull \hbox (badness 3514) in paragraph at lines 27240--27245 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1657] [1658] Underfull \hbox (badness 6691) in paragraph at lines 27332--27337 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 4024) in paragraph at lines 27862--27865 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 5431) in paragraph at lines 28468--28470 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1676] [1677] [1678] [1679] Underfull \hbox (badness 5431) in paragraph at lines 28678--28681 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1680] [1681] [1682] [1683] [1684] Underfull \hbox (badness 1337) in paragraph at lines 28992--28996 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1685] [1686] [1687] [1688] Underfull \hbox (badness 1616) in paragraph at lines 29294--29297 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1689] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] Underfull \hbox (badness 3557) in paragraph at lines 30424--30428 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4 /m/n/10 interval = [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] [1710] [1711] Underfull \hbox (badness 1337) in paragraph at lines 30788--30792 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1712] [1713] [1714] [1715] [1716] [1717] [1718] [1719] Underfull \hbox (badness 1337) in paragraph at lines 31315--31319 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728]) (./stats4-pkg.tex Chapter 11. [1729] [1730] [1731] [1732] [1733] [1734]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1735] [1736] [1737]) (./tcltk-pkg.tex [1738] Chapter 12. [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758]) (./tools-pkg.tex Chapter 13. [1759] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1760] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1761] [1762] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1763] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1764] [1765] [1766] [1767] [1768] [1769] [1770] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1776] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1777] [1778] [1779] [1780] [1781] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1782] [1783] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1784] Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1785] [1786] [1787]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1788] [1789] [1790] [1791] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1792] [1793] [1794] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1795] [1796] [1797] [1798] [1799] [1800] [1801] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2837. [1802] [1803] [1804] [1805] Underfull \hbox (badness 1424) in paragraph at lines 3119--3121 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] Underfull \hbox (badness 10000) in paragraph at lines 3823--3825 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1816] [1817] Underfull \hbox (badness 10000) in paragraph at lines 3962--3965 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1818] Underfull \hbox (badness 1137) in paragraph at lines 4064--4066 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1819] [1820] [1821] [1822] [1823] Underfull \hbox (badness 1796) in paragraph at lines 4372--4377 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type == [1824] Underfull \hbox (badness 1838) in paragraph at lines 4446--4452 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4446--4452 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1825] [1826] [1827] Underfull \hbox (badness 2197) in paragraph at lines 4662--4672 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : [1828] Underfull \hbox (badness 1571) in paragraph at lines 4725--4729 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1829] [1830] [1831]) (./utils-pkg.tex [1832] Chapter 14. Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1838] [1839] [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1843] [1844] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1845] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1846] [1847] [1848] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1865] [1866] [1867] [1868] [1869]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.clipboard}) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [1870] [1871] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1872] [1873] [1874] [1875] [1876] [1877] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](...,header = TRUE,sep = [1878] [1879] [1880] [1881] [1882] [1883] [1884] [1885] [1886] [1887] [1888] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1889] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1890] [1891] Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]pdfTeX war ning (ext4): destination with the same identifier (name{Rfn.format}) has been a lready used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] [1918] Underfull \hbox (badness 1371) in paragraph at lines 5996--5998 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1919] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1923] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1924] [1925] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1926] [1927] Underfull \hbox (badness 1325) in paragraph at lines 6632--6636 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [1928] Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [1929] Underfull \hbox (badness 3219) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6792--6799 [][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [1930] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from [1954] Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [1962] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] Underfull \vbox (badness 5533) has occurred while \output is active [1972] [1973] [1974] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [1975] [1976] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [1985] Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 11163--11167 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able [1998] Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [1999] [2000] [2001] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2002] [2003] [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2006] [2007] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2008] Underfull \hbox (badness 4779) in paragraph at lines 12237--12239 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a nd Underfull \hbox (badness 1077) in paragraph at lines 12267--12274 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2009] [2010] [2011] [2012] [2013] [2014] Underfull \hbox (badness 3780) in paragraph at lines 12668--12672 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 12684--12687 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2015] [2016] [2017] Underfull \hbox (badness 2302) in paragraph at lines 12889--12891 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13185--13190 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13194--13197 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2023] Underfull \vbox (badness 10000) has occurred while \output is active [2024] [2025] [2026] [2027] [2028] Underfull \hbox (badness 2932) in paragraph at lines 13614--13621 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 13614--13621 \T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [2029] [2030] [2031] [2032] Underfull \hbox (badness 6510) in paragraph at lines 13923--13927 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 13930--13933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 13930--13933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 14594--14599 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 14594--14599 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and [2042] Underfull \hbox (badness 1052) in paragraph at lines 14600--14602 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 14659--14662 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] Underfull \hbox (badness 10000) in paragraph at lines 15432--15434 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/zi4/m/sl/10 file = [2055] [2056] [2057]) [2058] [2059] [2060] (./KernSmooth-pkg.tex Chapter 15. [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070]) (./MASS-pkg.tex Chapter 16. [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] Underfull \hbox (badness 7944) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an d graph-i-cal pa-ram-e-ters. Note that [2108] [2109] [2110] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm /m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative [2111] [2112] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] Underfull \hbox (badness 1117) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2138] Underfull \hbox (badness 1117) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2156] [2157] [2158] [2159] [2160] Underfull \vbox (badness 10000) has occurred while \output is active [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] Underfull \hbox (badness 1117) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm \T1/zi4/m/sl/10 response ~ [2169] Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2170] [2171] [2172] Underfull \hbox (badness 6775) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n ant com-po-nents are used (ex-cept for [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]) (./Matrix-pkg.tex 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 [2219] 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 [2220] [2221] [2222] [2223] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2224] [2225] Underfull \hbox (badness 2418) in paragraph at lines 597--600 []\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a [2226] [2227] [2228] [2229] [2230] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a-lently, \T1/zi4/m/sl/10 to = [2231] [2232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} Underfull \hbox (badness 1117) in paragraph at lines 1189--1195 \T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t he same al-go-rithm [2233pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol ,dsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works viapdfTeX warning ( ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth od}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1209 \item[chol] \code{signature(x = "dgeMatrix")}: works via] [2234] [2235] Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2236] [2237] Underfull \hbox (badness 1097) in paragraph at lines 1560--1563 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 " dgeMatrix"\T1/ptm/m/n/10 , by class Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2238]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2239] [2240] [2241] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2242] [2243] [2244] [2245] [2246] Underfull \hbox (badness 1360) in paragraph at lines 2295--2299 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via [2247] [2248] [2249] [2250] Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble [2251] [2252] Underfull \hbox (badness 6842) in paragraph at lines 2700--2703 []\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T 1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[] [][] \T1/ptm/m/n/10 (with ``su-per-class'' [2253] Underfull \hbox (badness 10000) in paragraph at lines 2986--2990 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro up meth-ods re-turn a [2254] [2255] [2256] Underfull \hbox (badness 1173) in paragraph at lines 3196--3198 []\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2257] [2258] Underfull \hbox (badness 1354) in paragraph at lines 3442--3445 []\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex -plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in -her-it-ing from [2259] [2260] [2261] [2262] [2263] Underfull \hbox (badness 6188) in paragraph at lines 3852--3855 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = Underfull \hbox (badness 5147) in paragraph at lines 3855--3858 []\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 , or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type = [2264] [2265] Underfull \hbox (badness 2318) in paragraph at lines 3969--3973 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi 4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 , [2266] [2267] Underfull \hbox (badness 5245) in paragraph at lines 4105--4109 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1 0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x) [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (3.77782pt too wide) in paragraph at lines 4527--4527 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (48.77782pt too wide) in paragraph at lines 4530--4530 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] [2274] [2275] Underfull \hbox (badness 1931) in paragraph at lines 4762--4764 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/ ptm/m/n/10 codes should be aligned, see [2276] [2277] [2278] [2279] [2280] Underfull \hbox (badness 1005) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA \T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1655) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4 /m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2281] Overfull \hbox (42.75635pt too wide) in paragraph at lines 5134--5134 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2282] Underfull \hbox (badness 3229) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2283] Underfull \hbox (badness 4995) in paragraph at lines 5282--5285 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low Underfull \hbox (badness 10000) in paragraph at lines 5292--5295 []\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional [2284] [2285] [2286] [2287] [2288] Underfull \hbox (badness 1014) in paragraph at lines 5669--5672 []\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10 is a tri-an-gu-lar ma-trix. Anal-o-gously, [2289] [2290] [2291] [2292] Underfull \hbox (badness 10000) in paragraph at lines 5984--5987 []\T1/zi4/m/sl/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 [2293] Underfull \hbox (badness 2478) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde nseMatrix"\T1/ptm/m/n/10 . Class [2294] Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2295] Underfull \hbox (badness 10000) in paragraph at lines 6296--6299 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2296] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2297] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2298] Underfull \hbox (badness 2050) in paragraph at lines 6545--6548 []\T1/zi4/m/sl/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 [2299] [2300] [2301] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2302] Underfull \hbox (badness 6268) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1 0 . How-ever, [2303]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1527) in paragraph at lines 6961--6963 []\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \ T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 6966--6969 []\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1 /zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 [2304]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2305pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod.Rdash.methods}) has be en already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7356 ] [2306] Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 1448) in paragraph at lines 7426--7431 \T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an Underfull \hbox (badness 1264) in paragraph at lines 7441--7442 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures, see [2307] [2308] Underfull \hbox (badness 1430) in paragraph at lines 7585--7590 []\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1 /zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][] \T1/ptm/m/n/10 , and [2309] Underfull \hbox (badness 10000) in paragraph at lines 7656--7659 []\T1/zi4/m/sl/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 [2310] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X [2311] [2312] Underfull \vbox (badness 10000) has occurred while \output is active [2313] Underfull \hbox (badness 2478) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly . Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde nseMatrix"\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); use, e.g., [2314] [2315] Underfull \hbox (badness 5924) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim-ple meth-ods [2316]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2317] [2318] Underfull \hbox (badness 10000) in paragraph at lines 8427--8430 []\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2319] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2320] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u se, e.g., [2321] Underfull \vbox (badness 10000) has occurred while \output is active [2322] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 8724--8727 []\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a user con-ve-nience, to al-low [2323] [2324] [2325] [2326]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2327] [2328] [2329] [2330]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.rcond}) has been already u sed, duplicate ignored \relax l.9252 ... the Reciprocal Condition Number}{rcond} [2331] [2332] [2333] [2334] Underfull \hbox (badness 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1852) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][]( nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 --- Underfull \hbox (badness 2343) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.solve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} [2339] Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse = [2340] Underfull \hbox (badness 4403) in paragraph at lines 10053--10056 []\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing \T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame [2341] Underfull \hbox (badness 10000) in paragraph at lines 10159--10162 []\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co -er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] Underfull \hbox (badness 10000) in paragraph at lines 10758--10766 []\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 10758--10766 \T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca -tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [2350]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr. Q}) has been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2351] [2352] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2353] [2354] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/ m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2355] Underfull \vbox (badness 10000) has occurred while \output is active [2356] [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/ sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be [2359] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2360] [2361] Underfull \hbox (badness 1831) in paragraph at lines 11740--11746 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1 /zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar e de-fined [2362] Underfull \hbox (badness 1902) in paragraph at lines 11775--11779 []\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a nd other [2363] [2364] [2365] [2366] [2367] [2368] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2369] [2370] [2371]) (./boot-pkg.tex [2372] Chapter 18. [2373] [2374] [2375] [2376] [2377] [2378] [2379] [2380] [2381] [2382] Underfull \hbox (badness 1297) in paragraph at lines 797--807 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour [2383] 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. [2384] Underfull \vbox (badness 10000) has occurred while \output is active [2385] [2386] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 1859) in paragraph at lines 1066--1070 \T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will [2387] 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 [2388] [2389] [2390] [2391] 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- [2392] [2393] [2394] [2395] [2396] [2397] Underfull \hbox (badness 1005) in paragraph at lines 1797--1804 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 " ordinary" \T1/ptm/m/n/10 (case re-sam-pling), [2398] [2399] Underfull \vbox (badness 10000) has occurred while \output is active [2400] Underfull \hbox (badness 7379) 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. [2401] [2402] [2403] [2404] 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 [2405] 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. [2406] [2407] Underfull \hbox (badness 2970) 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/zi4/m/s l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t he sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl /10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n /10 is used. This is mul-ti-plied by [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] 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 [2431] [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] 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 [2442] [2443] [2444] [2445] 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 [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] [2455] [2456] Underfull \hbox (badness 4954) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa ddle.distn"\T1/ptm/m/n/10 . See the help file for [2457] [2458] [2459] [2460] [2461] [2462] [2463] [2464] [2465] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475]) (./class-pkg.tex [2476] Chapter 19. [2477] [2478] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492]) (./cluster-pkg.tex Chapter 20. [2493] [2494] [2495] [2496] [2497] Underfull \vbox (badness 7777) has occurred while \output is active [2498] [2499] [2500] [2501] [2502] Underfull \hbox (badness 4144) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem -ory (and hence time), but dis-ables [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2506] [2507] Underfull \hbox (badness 10000) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2508] [2509] [2510] Underfull \hbox (badness 6110) in paragraph at lines 1189--1193 []\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/ m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne nt, e.g., for [2511] [2512] [2513] Underfull \hbox (badness 10000) in paragraph at lines 1458--1461 [2514] [2515] Underfull \hbox (badness 2503) in paragraph at lines 1570--1573 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 2161--2164 Underfull \hbox (badness 10000) in paragraph at lines 2175--2181 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell ipsoid \T1/ptm/m/n/10 ob-jects. [2524] [2525] [2526] [2527] Underfull \hbox (badness 6675) in paragraph at lines 2410--2412 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2528] [2529] [2530] [2531] [2532] [2533] [2534] Underfull \hbox (badness 2980) in paragraph at lines 2901--2905 [][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [2535] [2536] [2537] [2538] [2539] Underfull \hbox (badness 1142) in paragraph at lines 3242--3245 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2540] [2541] Underfull \hbox (badness 1142) in paragraph at lines 3361--3364 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/ ptm/m/n/10 ) may also be sup-plied and are passed to [2542] [2543] [2544] [2545] Underfull \hbox (badness 2582) in paragraph at lines 3584--3589 [][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi 4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p tm/m/n/10 , [2546] Underfull \hbox (badness 3209) in paragraph at lines 3646--3651 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi 4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which Underfull \hbox (badness 8019) in paragraph at lines 3646--3651 \T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/ m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx [2547] [2548] [2549] [2550] Underfull \hbox (badness 10000) in paragraph at lines 3938--3940 []\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T 1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2551] [2552] [2553] [2554] Underfull \hbox (badness 2626) in paragraph at lines 4162--4167 []\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/ n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col = [2555] Underfull \hbox (badness 1383) in paragraph at lines 4240--4245 []\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m /it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T 1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2556] [2557] [2558] [2559] [2560] [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 4668--4670 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2563]) (./codetools-pkg.tex [2564] Chapter 21. [2565] [2566] [2567] [2568] [2569]) (./foreign-pkg.tex [2570] Chapter 22. [2571] [2572] [2573] [2574] [2575] [2576] [2577] [2578] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de -fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to [2579] Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 813--814 [2583] [2584] [2585] [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign :::writeForeignStata\T1/ptm/m/n/10 , [2590] [2591]) (./lattice-pkg.tex [2592] Chapter 23. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603] [2604] [2605] [2606] [2607] [2608] Underfull \hbox (badness 1062) in paragraph at lines 1398--1402 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2609] Underfull \vbox (badness 4416) has occurred while \output is active [2610] Underfull \hbox (badness 1803) in paragraph at lines 1566--1583 [][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack- age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 strip.default[][][]\T1/ptm/m/n/10 , [2611] [2612] [2613] Underfull \hbox (badness 3009) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][ ][]\T1/ptm/m/n/10 , which may pass them on to 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 [2614] [2615] [2616] [2617] [2618] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, the value of [2619] [2620] [2621] [2622] [2623] [2624] [2625] [2626] [2627] [2628] Underfull \hbox (badness 2781) in paragraph at lines 2848--2850 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col. regions \T1/ptm/m/n/10 ar-gu-ment in [2629] Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2630] [2631] [2632] [2633] [2634] [2635] [2636]pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.parallel}) has been already used, duplic ate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} [2637] [2638] [2639] [2640] [2641] [2642] [2643] Underfull \hbox (badness 5696) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2644] [2645] Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2646] [2647] [2648] Underfull \hbox (badness 3492) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p lot.polygon \T1/ptm/m/n/10 and [2649] [2650] [2651] [2652] [2653] [2654] [2655] [2656] [2657] [2658] Underfull \hbox (badness 6157) in paragraph at lines 5035--5038 []\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and [2659] [2660] [2661] [2662] [2663] [2664] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5486--5489 \T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le ft of pan-els us-ing [2665] [2666] [2667] [2668] [2669] Underfull \hbox (badness 4805) in paragraph at lines 5846--5850 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t ra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 5857--5864 \T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z i4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar e used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 5857--5864 [][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th e cho-sen view-port if so re-quested. [2670] [2671] [2672] [2673] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6157--6162 \T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there is no group-ing vari-able, oth-er-wise [2674] [2675] Underfull \hbox (badness 2310) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/ 10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round if [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 3168) in paragraph at lines 7055--7059 \T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U se [2687] [2688] [2689] [2690] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2691] [2692] Underfull \hbox (badness 3333) in paragraph at lines 7498--7500 []\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing [2693] [2694] [2695] Underfull \vbox (badness 10000) has occurred while \output is active [2696] [2697] [2698] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp ose \T1/ptm/m/n/10 from [2707] Underfull \hbox (badness 1092) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally con- [2708] [2709] Underfull \hbox (badness 3895) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T 1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2710] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2711] [2712] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 8876--8879 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c omponents.default \T1/ptm/m/n/10 and [2713] [2714] [2715] [2716] Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4 /m/sl/10 left,right,left.name,right.name,condition [2717] [2718] [2719] [2720] [2721] [2722] [2723] Underfull \hbox (badness 2310) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p tm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m /n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 , [2724] [2725] [2726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2727] [2728] [2729] Underfull \hbox (badness 4144) in paragraph at lines 10077--10080 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10077--10080 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2730] [2731]) (./mgcv-pkg.tex [2732] Chapter 24. [2733] [2734] [2735] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2736] [2737] [2738] [2739] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/ n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 365--372 [][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][] []\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][] \T1/ptm/m/n/10 , [2740] [2741] [2742] [2743] [2744] [2745] [2746] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2747] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2748] Underfull \vbox (badness 10000) has occurred while \output is active [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] Underfull \hbox (badness 1142) in paragraph at lines 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2772] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2773] [2774] [2775] [2776] [2777] Underfull \vbox (badness 10000) has occurred while \output is active [2778] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \vbox (badness 10000) has occurred while \output is active [2780] [2781] [2782] [2783] [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] Underfull \hbox (badness 10000) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/ n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2794] [2795] Underfull \vbox (badness 10000) has occurred while \output is active [2796] [2797] [2798] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2799] [2800] [2801] [2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2811] Underfull \hbox (badness 1231) in paragraph at lines 4692--4694 []\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with [2812] [2813] [2814] Underfull \vbox (badness 10000) has occurred while \output is active [2815] [2816] [2817] Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2818] [2819] [2820] [2821] [2822] [2823] [2824] Underfull \hbox (badness 10000) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(... ,fit=FALSE) \T1/ptm/m/n/10 or [2825] [2826] Underfull \vbox (badness 10000) has occurred while \output is active [2827] [2828] [2829] [2830] [2831] [2832] [2833] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2834] [2835] [2836] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] Underfull \hbox (badness 1087) in paragraph at lines 6326--6327 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas e, and if [2841] [2842] [2843] Underfull \vbox (badness 10000) has occurred while \output is active [2844] Underfull \vbox (badness 10000) has occurred while \output is active [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] [2867] Underfull \hbox (badness 6001) in paragraph at lines 7912--7914 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] Underfull \hbox (badness 1038) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim. pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/ sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 , [2880] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 , [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] Underfull \hbox (badness 1852) in paragraph at lines 9387--9390 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2892] [2893] [2894] Underfull \hbox (badness 1852) in paragraph at lines 9551--9554 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[] [][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at- tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and [2895] [2896] Underfull \vbox (badness 10000) has occurred while \output is active [2897] [2898] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2899] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2900] [2901] [2902] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2903] [2904] [2905] [2906] Underfull \hbox (badness 4792) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/ 10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m /n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2907] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1 0 "deviance"\T1/ptm/m/n/10 , [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [2919] [2920] Underfull \hbox (badness 1320) in paragraph at lines 11084--11089 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T 1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If ma- [2921] [2922] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2923] Underfull \hbox (badness 1762) in paragraph at lines 11279--11291 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T 1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr es-sion splines with [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Underfull \hbox (badness 7667) in paragraph at lines 11491--11497 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2934] [2935] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2936] [2937] Underfull \hbox (badness 1436) in paragraph at lines 12074--12081 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one [2938] [2939] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 12754--12760 \T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T 1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] [2955] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2956] [2957] [2958] [2959] Underfull \hbox (badness 3895) in paragraph at lines 13358--13361 [][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2960] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2961] [2962] [2963] [2964] Underfull \hbox (badness 1371) in paragraph at lines 13620--13626 []\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/ zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de fined.smooth[][][]\T1/ptm/m/n/10 , Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664 [][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4 /m/sl/10 factor.smooth.interaction[][][] [2965] [2966] [2967] [2968] Underfull \hbox (badness 2326) in paragraph at lines 13865--13872 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and [2969] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978] [2979] [2980] Underfull \vbox (badness 10000) has occurred while \output is active [2981] [2982] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] Underfull \hbox (badness 1796) in paragraph at lines 15594--15597 []\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/ sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar [2997] [2998] [2999] [3000] [3001] [3002]) (./nlme-pkg.tex Chapter 25. [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 2875) in paragraph at lines 1994--2000 []\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat- ing a co-vari-ate Underfull \hbox (badness 1466) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1 0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] Underfull \hbox (badness 10000) in paragraph at lines 2256--2262 [][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi alize.corStruct[][][]\T1/ptm/m/n/10 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 1067) in paragraph at lines 4414--4419 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3070] [3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/ m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo variate.varFunc[][][]\T1/ptm/m/n/10 , [3082] [3083] [3084] [3085] [3086] [3087] [3088] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 , [3089] [3090] [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 10000) in paragraph at lines 5973--5978 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou psFormula.lme[][][]\T1/ptm/m/n/10 , [3096] [3097] [3098] [3099] Underfull \hbox (badness 1490) in paragraph at lines 6243--6254 [][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot. gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 , [3100] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3101] [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3107] [3108] [3109] [3110] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n /10 , [3111] [3112] [3113] [3114] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/ sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize .glsStruct[][][]\T1/ptm/m/n/10 , [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3134]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig ma}) has been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3135] [3136] [3137] [3138] Underfull \hbox (badness 10000) in paragraph at lines 8802--8809 [][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[] [][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/ 10 , [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1 /ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T 1/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik .lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm /m/n/10 , [3147] [3148] [3149] [3150] [3151]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3164] [3165] Underfull \hbox (badness 1490) in paragraph at lines 10597--10603 [][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n /10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1286) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl /10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] Underfull \hbox (badness 1067) in paragraph at lines 15888--15893 \T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues ), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to [3244] [3245] [3246] [3247] Underfull \hbox (badness 1448) in paragraph at lines 16131--16140 \T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3248] [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3258] [3259] [3260] [3261] [3262] Underfull \hbox (badness 8056) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/ m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural Underfull \hbox (badness 5756) in paragraph at lines 17171--17180 \T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T 1/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for [3263] Underfull \hbox (badness 2913) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower \T1/ptm/m/n/10 , [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl /10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10 , [3275] [3276] [3277] [3278] [3279] Underfull \hbox (badness 5036) in paragraph at lines 18341--18350 [][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/ m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4 /m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] [3290] [3291] [3292]) (./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} [3293] Underfull \hbox (badness 1117) 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 \T1/zi4/m/sl/10 response ~ [3294] [3295] [3296] [3297] [3298] [3299] [3300]) (./rpart-pkg.tex Chapter 27. [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./spatial-pkg.tex [3330] Chapter 28. [3331] [3332] [3333] [3334] [3335] [3336] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3337] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349]) (./survival-pkg.tex [3350] Chapter 29. [3351] [3352] [3353] [3354]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3355] [3356] [3357] [3358] [3359] Underfull \vbox (badness 10000) has occurred while \output is active [3360] [3361] [3362] [3363] [3364] [3365] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3366] [3367] [3368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391] [3392] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3393] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3394] [3395] [3396] Underfull \vbox (badness 10000) has occurred while \output is active [3397] Underfull \vbox (badness 10000) has occurred while \output is active [3398] [3399] [3400] [3401] [3402] [3403] [3404] Underfull \vbox (badness 10000) has occurred while \output is active [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] Underfull \hbox (badness 5274) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "summary.survfit"\T1/ptm/m /n/10 , which is the re-sult of the [3418] [3419] [3420] [3421] [3422] [3423] [3424] [3425] [3426] [3427] [3428] Underfull \vbox (badness 2126) has occurred while \output is active [3429] [3430] [3431] Underfull \hbox (badness 1281) in paragraph at lines 5560--5563 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/zi4/m/sl/10 "response "\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d fbeta"\T1/ptm/m/n/10 , [3432] [3433] [3434] [3435] [3436]pdfTeX warning (ext4): destination with the s ame identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3453] [3454] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3455] [3456] [3457] [3458] [3459] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T 1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 , [3460] [3461] [3462] [3463] [3464] Underfull \hbox (badness 1389) in paragraph at lines 7911--7921 []\T1/ptm/m/n/10 One of \T1/zi4/m/sl/10 "none"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "plain"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log" \T1/ptm/m/n/10 (the de-fault), \T 1/zi4/m/sl/10 "log-log" \T1/ptm/m/n/10 or [3465] [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3471] [3472] [3473] [3474] [3475] Underfull \vbox (badness 10000) has occurred while \output is active [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493]) [3494] (./fullrefman.ind [3495] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504] [3505] [3506] [3507] [3508] [3509] [3510] [3511] [3512] [3513] [3514] [3515] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2229--2231 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [3516] [3517] [3518] [3519] [3520] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2795--2797 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [3521] [3522] [3523] [3524] [3525] [3526] [3527] [3528] [3529] Overfull \hbox (20.8567pt too wide) in paragraph at lines 3939--3941 []\T1/zi4/m/it/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 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[3543] [3544] [3545] Overfull \hbox (0.8567pt too wide) in paragraph at lines 6616--6618 []\T1/zi4/m/it/10 cbind2,denseMatrix,sparseMatrix-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 6618--6620 []\T1/zi4/m/it/10 cbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 6648--6650 []\T1/zi4/m/it/10 cbind2,sparseMatrix,denseMatrix-method [3546] Overfull \hbox (15.8567pt too wide) in paragraph at lines 6650--6652 []\T1/zi4/m/it/10 cbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 6656--6658 []\T1/zi4/m/it/10 cbind2,sparseMatrix,sparseMatrix-method [3547] [3548] [3549] Overfull \hbox (10.8567pt too wide) in paragraph at lines 7378--7380 []\T1/zi4/m/it/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 7380--7382 []\T1/zi4/m/it/10 coerce,atomicVector,sparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 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Transcript written on fullrefman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texlive/texmf-dist/font s/map/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [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] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 359203 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texlive/texmf-dist/font s/map/pdftex/updmap/pdftex.map}] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [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] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 375758 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/usr/share/texlive/texmf-dist/font s/map/pdftex/updmap/pdftex.map}] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [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] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 375761 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Underfull \hbox (badness 7685) in paragraph at lines 1322--1326 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1539--1543 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [17] [18] Chapter 4 [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1917--1929 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37] [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3371--3371 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4985--4985 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 4992--4992 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5096--5096 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [60] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5133--5133 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] [63] [64] [65] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5578--5578 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [66] [67] Appendix D [68] [69] [70] (Function and variable index) [71] No file R-admin.vrs. (Concept index) [72] No file R-admin.cps. (Environment variable index) [73] No file R-admin.ens. [74] ) (see the transcript file for additional information) Output written on R-admin.pdf (77 pages, 469749 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.toc [-1] [-2]) [-3] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Underfull \hbox (badness 7685) in paragraph at lines 1322--1326 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1539--1543 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [17] [18] Chapter 4 [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1917--1929 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37] [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3371--3371 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4985--4985 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 4992--4992 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5096--5096 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [60] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5133--5133 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] [63] [64] [65] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5578--5578 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [66] [67] Appendix D [68] [69] [70] (Function and variable index) [71] (Concept index) [72] (Environment variable index) [73] [74] ) (see the transcript file for additional information) Output written on R-admin.pdf (79 pages, 514693 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4 [15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23] [24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29] (Function and variable index) [30] No file R-data.vrs. (Concept index) [31] No file R-data.cps. [32] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 270423 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc [-1]) [-2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc) (Acknowledgements) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4 [15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23] [24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29] (Function and variable index) [30] [31] (Concept index) [32] [33] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 310031 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc [-1]) [-2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.toc) (Acknowledgements) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4 [15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23] [24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29] (Function and variable index) [30] [31] (Concept index) [32] [33] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 310041 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7100--7106 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8395--8404 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8832--8834 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Chapter 5 [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [118] [119] [120] [121] [122] [123] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 11534--11536 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [147] [148] Chapter 6 [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] Warning: unbalanced parentheses in @def... [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 10000) in paragraph at lines 14383--14389 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [168] [169] Chapter 8 [170] [171] [172] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [173] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15357--15364 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15480--15484 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [182] No file R-exts.vrs. (Concept index) [183] No file R-exts.cps. [184] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (187 pages, 895197 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (Acknowledgements) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7100--7106 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8395--8404 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8832--8834 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Chapter 5 [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [118] [119] [120] [121] [122] [123] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 11534--11536 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [147] [148] Chapter 6 [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] Warning: unbalanced parentheses in @def... [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 10000) in paragraph at lines 14383--14389 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [168] [169] Chapter 8 [170] [171] [172] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [173] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15357--15364 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15480--15484 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [182] [183] [184] [185] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [186] [187] [188] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (194 pages, 958457 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (Acknowledgements) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7100--7106 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8395--8404 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8832--8834 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Chapter 5 [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [118] [119] [120] [121] [122] [123] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 11534--11536 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [147] [148] Chapter 6 [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] Warning: unbalanced parentheses in @def... [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 10000) in paragraph at lines 14383--14389 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [168] [169] Chapter 8 [170] [171] [172] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [173] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15357--15364 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15480--15484 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [182] [183] [184] [185] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [186] [187] [188] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (194 pages, 958448 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [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] [34] [35] [36] [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] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] No file R-intro.vrs. Appendix E [94] No file R-intro.cps. Appendix F [95] [96] ) (see the transcript file for additional information) Output written on R-intro.pdf (99 pages, 571568 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (Preface) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [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] [34] [35] [36] [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] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 621211 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (Preface) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [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] [34] [35] [36] [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] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 621222 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] No file R-ints.vrs. (Concept index) [62] No file R-ints.cps. [63] ) (see the transcript file for additional information) Output written on R-ints.pdf (66 pages, 397962 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc [-1]) [-2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] ) (see the transcript file for additional information) Output written on R-ints.pdf (68 pages, 448496 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc [-1]) [-2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] ) (see the transcript file for additional information) Output written on R-ints.pdf (68 pages, 448491 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] No file R-lang.vrs. (Concept Index) [52] No file R-lang.cps. Appendix A [53] [54] ) (see the transcript file for additional information) Output written on R-lang.pdf (57 pages, 326405 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc [-1] [-2]) [-3] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374849 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc [-1] [-2]) [-3] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.toc) Chapter 1 (/builddir/build/BUILD/R-3.6.0/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374851 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc' Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DyyZ43 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 + cd R-3.6.0 + make DESTDIR=/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 install install-info mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/m4' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/m4' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/tools' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/tools' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc' installing doc ... mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/R mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/man/man1 make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/html' installing doc/html ... mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/R/html make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/html' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' installing doc/manual ... mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/R/manual mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/R/manual/images make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/etc' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/etc installing etc ... make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/etc' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/share' installing share ... mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/R mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/dictionaries mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/encodings mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/java mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/licenses mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/make mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/Rd mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/Rd/macros mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/sh mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/texmf mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/texmf/bibtex/bib mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/texmf/bibtex/bst mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/R/texmf/tex/latex make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/share' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/scripts' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/bin mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/scripts' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/include/R make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include/R_ext' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/include/R/R_ext make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include/R_ext' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/lib make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/blas' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/tre' make[3]: Nothing to be done for 'install'. BUILDSTDERR: make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/sr+ mv doc/manual/R-exts.texi.spot doc/manual/R-exts.texi + mv doc/manual/R-intro.texi.spot doc/manual/R-intro.texi + make DESTDIR=/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 install-pdf c/extra/tre' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/tzone' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/tzone' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/xdr' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/extra/intl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra/intl' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/extra' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/appl' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/appl' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/nmath' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/nmath' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -DR_HOME='"/usr/lib64/R"' \ -o Rscript ./Rscript.c mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/pkgconfig make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/unix' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/exec make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/main' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/main' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/modules make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/internet' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/lapack' make[3]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[3]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules/X11' make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/modules' make[2]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/library' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library installing packages ... building HTML index ... make[2]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/library' make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/tests' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/tests' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' mkdir -p -- /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/info /usr/bin/install -c -m 644 "./dir" "/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/info" installing R info pages ... updating '/usr/share/info/dir' ... make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.toc) (Acknowledgements) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7100--7106 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8395--8404 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8672--8673 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8804--8804 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8832--8834 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8964--8964 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Chapter 5 [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10111--10111 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [118] [119] [120] [121] [122] [123] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10691--10691 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 11534--11536 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12572--12572 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [147] [148] Chapter 6 [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] Warning: unbalanced parentheses in @def... [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 10000) in paragraph at lines 14383--14389 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [168] [169] Chapter 8 [170] [171] [172] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14795--14795 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [173] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14854--14854 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15357--15364 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15480--15484 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [182] [183] [184] [185] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [186] [187] [188] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (194 pages, 958448 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-03-10.14]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/builddir/build/BUILD/R-3.6.0/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/builddir/build/BUILD/R-3.6.0/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/builddir/build/BUILD/R-3.6.0/doc/manual/version.texi) [1{/usr/share/texlive/t exmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.toc) (Preface) (/builddir/build/BUILD/R-3.6.0/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [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] [34] [35] [36] [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] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 621222 bytes). Transcript written on R-intro.log. installing R manuals in PDF format ... make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/doc/manual' make[1]: Entering directory '/builddir/build/BUILD/R-3.6.0/src/include' make[1]: 'Rmath.h' is up to date. make[1]: Leaving directory '/builddir/build/BUILD/R-3.6.0/src/include' ~/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R ~/build/BUILD/R-3.6.0 ~/build/BUILD/R-3.6.0 ~/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/texmf/tex/latex ~/build/BUILD/R-3.6.0 ~/build/BUILD/R-3.6.0 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/bin/Rscript explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/Rscript explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/exec/R extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/bin/Rscript extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/Rscript explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/lib/libR.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/exec/R extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/lib/libR.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/lib/libRblas.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/KernSmooth/libs/KernSmooth.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/lib/libRlapack.so extracting debug info from 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/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/lattice/libs/lattice.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/methods/libs/methods.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/methods/libs/methods.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/mgcv/libs/mgcv.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/mgcv/libs/mgcv.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/nlme/libs/nlme.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/nlme/libs/nlme.so explicitly decompress any DWARF compressed ELF sections in 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/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/spatial/libs/spatial.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/splines/libs/splines.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/splines/libs/splines.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/stats/libs/stats.so BUILDSTDERR: extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-cpio: src/modules/lapack/SRC/iparam2stage.F: Cannot stat: No such file or directory BUILDSTDERR: 33688 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/bin/true 3.fc31.riscv64/usr/lib64/R/library/stats/libs/stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/survival/libs/survival.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/survival/libs/survival.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/tcltk/libs/tcltk.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/tcltk/libs/tcltk.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/tools/libs/tools.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/library/tools/libs/tools.so explicitly decompress any DWARF compressed ELF sections in 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/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/modules/lapack.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/modules/lapack.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/libRmath.so extracting debug info from /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/libRmath.so original debug info size: 34428kB, size after compression: 32020kB /usr/lib/rpm/sepdebugcrcfix: Updated 35 CRC32s, 0 CRC32s did match. Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.FNVMD6 Processing files: R-3.6.0-3.fc31.riscv64 Processing files: R-core-3.6.0-3.fc31.riscv64 BUILDSTDERR: warning: Duplicate build-ids /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/bin/Rscript and /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib64/R/bin/Rscript BUILDSTDERR: warning: absolute symlink: /usr/share/texmf/tex/latex/R -> /usr/share/R/texmf/tex/latex Provides: R(KernSmooth) = 2.23-15 R(MASS) = 7.3-51.4 R(Matrix) = 1.2-17 R(base) = 3.6.0 R(boot) = 1.3-22 R(class) = 7.3-15 R(cluster) = 2.0.8 R(codetools) = 0.2-16 R(compiler) = 3.6.0 R(datasets) = 3.6.0 R(foreign) = 0.8-71 R(grDevices) = 3.6.0 R(graphics) = 3.6.0 R(grid) = 3.6.0 R(lattice) = 0.20-38 R(methods) = 3.6.0 R(mgcv) = 1.8-28 R(nlme) = 3.1-139 R(nnet) = 7.3-12 R(parallel) = 3.6.0 R(rpart) = 4.1-15 R(spatial) = 7.3-11 R(splines) = 3.6.0 R(stats) = 3.6.0 R(stats4) = 3.6.0 R(survival) = 2.44-1.1 R(tcltk) = 3.6.0 R(tools) = 3.6.0 R(translations) = 3.6.0 R(utils) = 3.6.0 R-KernSmooth = 2.23.15 R-MASS = 7.3.51.4 R-Matrix = 1.2.17 R-base = 3.6.0 R-boot = 1.3.22 R-class = 7.3.15 R-cluster = 2.0.8 R-codetools = 0.2.16 R-compiler = 3.6.0 R-core = 3.6.0-3.fc31 R-core(riscv-64) = 3.6.0-3.fc31 R-datasets = 3.6.0 R-foreign = 0.8.71 R-grDevices = 3.6.0 R-graphics = 3.6.0 R-grid = 3.6.0 R-lattice = 0.20.38 R-methods = 3.6.0 R-mgcv = 1.8.28 R-nlme = 3.1.139 R-nnet = 7.3.12 R-parallel = 3.6.0 R-rpart = 4.1.15 R-spatial = 7.3.11 R-splines = 3.6.0 R-stats = 3.6.0 R-stats4 = 3.6.0 R-survival = 2.44.1.1 R-tcltk = 3.6.0 R-tools = 3.6.0 R-translations = 3.6.0 R-utils = 3.6.0 config(R-core) = 3.6.0-3.fc31 libR.so()(64bit) libRblas.so()(64bit) libRlapack.so()(64bit) Requires(interp): /bin/sh /bin/sh /bin/sh Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /bin/sh Requires(postun): /bin/sh Requires(posttrans): /bin/sh Requires: /bin/bash /bin/sh ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libRblas.so()(64bit) libRlapack.so()(64bit) libX11.so.6()(64bit) libXmu.so.6()(64bit) libXt.so.6()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libcairo.so.2()(64bit) libcurl.so.4()(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgfortran.so.5()(64bit) libgfortran.so.5(GFORTRAN_8)(64bit) libgobject-2.0.so.0()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libicui18n.so.62()(64bit) libicuuc.so.62()(64bit) libjpeg.so.62()(64bit) libjpeg.so.62(LIBJPEG_6.2)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpcre.so.1()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libreadline.so.8()(64bit) libtcl8.6.so()(64bit) libtiff.so.5()(64bit) libtiff.so.5(LIBTIFF_4.0)(64bit) libtk8.6.so()(64bit) libtre.so.5()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Obsoletes: R-Matrix < 0.999375-7 Processing files: R-core-devel-3.6.0-3.fc31.riscv64 Provides: R-Matrix-devel = 1.2.17 R-core-devel = 3.6.0-3.fc31 R-core-devel(riscv-64) = 3.6.0-3.fc31 pkgconfig(libR) = 3.6.0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config Obsoletes: R-Matrix-devel < 0.999375-7 Processing files: R-devel-3.6.0-3.fc31.riscv64 Processing files: R-java-3.6.0-3.fc31.riscv64 Processing files: R-java-devel-3.6.0-3.fc31.riscv64 Processing files: libRmath-3.6.0-3.fc31.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.nHH4H5 + umask 022 + cd /builddir/build/BUILD + cd R-3.6.0 + DOCDIR=/builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/libRmath + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/libRmath + cp -pr doc/COPYING /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/share/doc/libRmath + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Provides: libRmath = 3.6.0-3.fc31 libRmath(riscv-64) = 3.6.0-3.fc31 libRmath.so()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) rtld(GNU_HASH) Processing files: libRmath-devel-3.6.0-3.fc31.riscv64 Provides: libRmath-devel = 3.6.0-3.fc31 libRmath-devel(riscv-64) = 3.6.0-3.fc31 pkgconfig(libRmath) = 3.6.0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config Processing files: libRmath-static-3.6.0-3.fc31.riscv64 Provides: libRmath-static = 3.6.0-3.fc31 libRmath-static(riscv-64) = 3.6.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-debugsource-3.6.0-3.fc31.riscv64 Provides: R-debugsource = 3.6.0-3.fc31 R-debugsource(riscv-64) = 3.6.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-debuginfo-3.6.0-3.fc31.riscv64 Provides: R-debuginfo = 3.6.0-3.fc31 R-debuginfo(riscv-64) = 3.6.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-debugsource(riscv-64) = 3.6.0-3.fc31 Processing files: R-core-debuginfo-3.6.0-3.fc31.riscv64 BUILDSTDERR: warning: Duplicate build-ids /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib/debug/usr/bin/Rscript-3.6.0-3.fc31.riscv64.debug and /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64/usr/lib/debug/usr/lib64/R/bin/Rscript-3.6.0-3.fc31.riscv64.debug Provides: R-core-debuginfo = 3.6.0-3.fc31 R-core-debuginfo(riscv-64) = 3.6.0-3.fc31 debuginfo(build-id) = 054367d151b942698845fbfce2efa66ce67b3d2f debuginfo(build-id) = 12f6de3e3af8009820d25a4eec17ff2c27430497 debuginfo(build-id) = 19d01d9b4e4b6a4ddc45a56372e28dc9143ff7dd debuginfo(build-id) = 1a21b7667c0ce940afc6b3239fdcaaf062196d21 debuginfo(build-id) = 3548188872ff43b51f01ab0710fa4ef5d5c30432 debuginfo(build-id) = 39b5173f943d27e097b158eaf8d1e7a71d2a0731 debuginfo(build-id) = 3bc2e9cde00288959b1cda9779baf502c00e601a debuginfo(build-id) = 3f6e3c7bc9b1a24b05ddf444fe1e5f84f24c5af6 debuginfo(build-id) = 421440cd65bad2bfc1625849a58771c4d1d9dac3 debuginfo(build-id) = 48ca494b2bdeeb4dc2c7f7b88ebbb639ad3dbfed debuginfo(build-id) = 4b995011df25c30e3e995f825ae93e1528358c8b debuginfo(build-id) = 4e489193238eb9545ed1c27d6ca641325d4a9297 debuginfo(build-id) = 5719f5ea917526f2ee6c632f5a369826f95ed1f2 debuginfo(build-id) = 5cb7859fcd2b56ee501e21272c0b574fb5af496c debuginfo(build-id) = 5ce93b1cdd47e88272aa8f31d9e32ab6633569b2 debuginfo(build-id) = 698188059b760ea49bf4d3378ee6fe5076523a84 debuginfo(build-id) = 81577252dae1d2369fea38b6e428bb412d71ff35 debuginfo(build-id) = 8428d62c93335cb0a706a797a5a046936b75d940 debuginfo(build-id) = 8449889f327ee05570e7249ac484bce67cc9ea7f debuginfo(build-id) = 92f871f2ae5189d486878c1344c9e4e1622a17c6 debuginfo(build-id) = 9e36d35708406ea3d57066b0b3947342efcfff2e debuginfo(build-id) = a005557984a34e37001f25f336c5b239c58e27a6 debuginfo(build-id) = a29f617ae96b5e4f4dcaf7947f4d571f780ce9c8 debuginfo(build-id) = a978338c0cf83f81f9957c302afad67f8edcdafd debuginfo(build-id) = ab0afe07ba5a6df1329a90affd51bc8db2191284 debuginfo(build-id) = b142845b26c9ca68176e5450891b7af7607c1c19 debuginfo(build-id) = b17fd50a5e8ac8e96e8d024fbd3c07f8e92d55db debuginfo(build-id) = bba55df3d1bb9f576d4b7ad7640191a258aec403 debuginfo(build-id) = cae5d4aa9e596c3f76e0190060b20d91b61d3118 debuginfo(build-id) = d66e0b107009f3b3caa04430f18c326d33e11100 debuginfo(build-id) = dbfaf8c6c2cab1a21736e057ba75558f456c186f debuginfo(build-id) = e249c58621d0355e7cdecba7c7c968a419f828e3 debuginfo(build-id) = fe75386d0a0b9760af69142734e2d78e822949ab Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-debugsource(riscv-64) = 3.6.0-3.fc31 Processing files: libRmath-debuginfo-3.6.0-3.fc31.riscv64 Provides: debuginfo(build-id) = 6e1c057f78f333190a2ae26b874e4899e796be78 libRmath-debuginfo = 3.6.0-3.fc31 libRmath-debuginfo(riscv-64) = 3.6.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-debugsource(riscv-64) = 3.6.0-3.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 Wrote: /builddir/build/RPMS/R-devel-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-java-devel-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-java-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/libRmath-devel-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/libRmath-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-core-devel-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-debuginfo-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/libRmath-static-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/libRmath-debuginfo-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-debugsource-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-core-debuginfo-3.6.0-3.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-core-3.6.0-3.fc31.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.vVxtW2 + umask 022 + cd /builddir/build/BUILD + cd R-3.6.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-3.6.0-3.fc31.riscv64 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Child return code was: 0