Attachment 371097 Details for Bug 539007 – build.log

build.log

build.log (text/plain), 37.35 KB, created by FTBFS on 2009-11-19 16:24:37 UTC

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Creator: FTBFS

Created: 2009-11-19 16:24:37 UTC

Size: 37.35 KB

patch

obsolete

>Mock Version: 0.9.19
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-preprocessCore-1.6.0-2.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x2901890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Wrote: /builddir/build/SRPMS/R-preprocessCore-1.6.0-2.fc13.src.rpm
>Child returncode was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-preprocessCore-1.6.0-2.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x2901890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.LEwGZB
>+ umask 022
>+ cd /builddir/build/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /builddir/build/BUILD
>+ rm -rf preprocessCore
>+ /bin/mkdir -p preprocessCore
>+ cd preprocessCore
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/preprocessCore_1.6.0.tar.gz
>+ /bin/tar -xf -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.L1B0Hs
>+ exit 0
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd preprocessCore
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.bC9lAj
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64
>++ dirname /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64
>+ cd preprocessCore
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library
>+ R CMD INSTALL preprocessCore -l /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library
>* installing *source* package 'preprocessCore' ...
>checking for gcc... gcc
>checking for C compiler default output file name... a.out
>checking whether the C compiler works... yes
>checking whether we are cross compiling... no
>checking for suffix of executables... 
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether gcc accepts -g... yes
>checking for gcc option to accept ISO C89... none needed
>checking for pthread_create in -lpthread... yes
>checking if we can use pthreads... yes
>configure: creating ./config.status
>config.status: creating src/Makevars
>** libs
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_colSummarize.c -o R_colSummarize.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_plmd_interfaces.c -o R_plmd_interfaces.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_plmr_interfaces.c -o R_plmr_interfaces.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_rlm_interfaces.c -o R_rlm_interfaces.o
>R_rlm_interfaces.c: In function 'R_medianpolish_rma_default_model':
>R_rlm_interfaces.c:273: warning: unused variable 'se'
>R_rlm_interfaces.c:272: warning: unused variable 'weights'
>R_rlm_interfaces.c: In function 'R_rlm_rma_given_probe_effects':
>R_rlm_interfaces.c:391: warning: unused variable 'i'
>R_rlm_interfaces.c: In function 'R_wrlm_rma_given_probe_effects':
>R_rlm_interfaces.c:475: warning: unused variable 'i'
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_subColSummarize.c -o R_subColSummarize.o
>R_subColSummarize.c: In function 'subColSummarize_avg_log_group':
>R_subColSummarize.c:81: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_avg_log':
>R_subColSummarize.c:102: warning: unused variable 'j'
>R_subColSummarize.c:100: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:96: warning: unused variable 'cur_rows'
>R_subColSummarize.c:94: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_log_avg_group':
>R_subColSummarize.c:248: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_log_avg':
>R_subColSummarize.c:266: warning: unused variable 'j'
>R_subColSummarize.c:264: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:260: warning: unused variable 'cur_rows'
>R_subColSummarize.c:258: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_avg_group':
>R_subColSummarize.c:415: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_avg':
>R_subColSummarize.c:433: warning: unused variable 'j'
>R_subColSummarize.c:431: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:427: warning: unused variable 'cur_rows'
>R_subColSummarize.c:425: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_biweight_log_group':
>R_subColSummarize.c:581: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_biweight_log':
>R_subColSummarize.c:601: warning: unused variable 'j'
>R_subColSummarize.c:599: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:595: warning: unused variable 'cur_rows'
>R_subColSummarize.c:593: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_biweight_group':
>R_subColSummarize.c:749: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_biweight':
>R_subColSummarize.c:768: warning: unused variable 'j'
>R_subColSummarize.c:766: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:762: warning: unused variable 'cur_rows'
>R_subColSummarize.c:760: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_median_log_group':
>R_subColSummarize.c:916: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_median_log':
>R_subColSummarize.c:936: warning: unused variable 'j'
>R_subColSummarize.c:934: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:930: warning: unused variable 'cur_rows'
>R_subColSummarize.c:928: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_log_median_group':
>R_subColSummarize.c:1083: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_log_median':
>R_subColSummarize.c:1102: warning: unused variable 'j'
>R_subColSummarize.c:1100: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:1096: warning: unused variable 'cur_rows'
>R_subColSummarize.c:1094: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_median_group':
>R_subColSummarize.c:1249: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_median':
>R_subColSummarize.c:1267: warning: unused variable 'j'
>R_subColSummarize.c:1265: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:1261: warning: unused variable 'cur_rows'
>R_subColSummarize.c:1259: warning: unused variable 'buffer'
>R_subColSummarize.c: In function 'subColSummarize_medianpolish_log_group':
>R_subColSummarize.c:1417: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_medianpolish_log':
>R_subColSummarize.c:1436: warning: unused variable 'j'
>R_subColSummarize.c:1434: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:1430: warning: unused variable 'cur_rows'
>R_subColSummarize.c: In function 'subColSummarize_medianpolish_group':
>R_subColSummarize.c:1587: warning: no return statement in function returning non-void
>R_subColSummarize.c: In function 'R_subColSummarize_medianpolish':
>R_subColSummarize.c:1606: warning: unused variable 'j'
>R_subColSummarize.c:1604: warning: unused variable 'ncur_rows'
>R_subColSummarize.c:1600: warning: unused variable 'cur_rows'
>R_subColSummarize.c:1598: warning: unused variable 'buffer2'
>R_subColSummarize.c:1598: warning: unused variable 'buffer'
>R_subColSummarize.c: At top level:
>R_subColSummarize.c:1563: warning: 'subColSummarize_medianpolish_group' defined but not used
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c avg.c -o avg.o
>avg.c: In function 'colaverage_no_copy':
>avg.c:90: warning: unused variable 'i'
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c avg_log.c -o avg_log.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c biweight.c -o biweight.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c init_package.c -o init_package.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c lm.c -o lm.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c log_avg.c -o log_avg.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c log_median.c -o log_median.o
>log_median.c: In function 'logmedian_no_copy':
>log_median.c:138: warning: unused variable 'i'
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c matrix_functions.c -o matrix_functions.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c median.c -o median.o
>median.c: In function 'colmedian_no_copy':
>median.c:146: warning: unused variable 'i'
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c median_log.c -o median_log.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c medianpolish.c -o medianpolish.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c plmd.c -o plmd.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c plmr.c -o plmr.o
>plmr.c:82: warning: 'XTWY_R' defined but not used
>plmr.c:152: warning: 'XTWX_R' defined but not used
>plmr.c:279: warning: 'XTWX_R_inv' defined but not used
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c psi_fns.c -o psi_fns.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c qnorm.c -o qnorm.o
>qnorm.c: In function 'qnorm_c_determine_target':
>qnorm.c:1813: warning: unused variable 'non_na'
>qnorm.c:1808: warning: unused variable 'j'
>qnorm.c: In function 'qnorm_c_determine_target_via_subset':
>qnorm.c:2396: warning: unused variable 'non_na'
>qnorm.c:2391: warning: unused variable 'j'
>qnorm.c: In function 'using_target_group_via_subset':
>qnorm.c:2837: warning: control reaches end of non-void function
>qnorm.c: In function 'determine_target_group_via_subset':
>qnorm.c:2381: warning: control reaches end of non-void function
>qnorm.c: In function 'determine_target_group':
>qnorm.c:1799: warning: control reaches end of non-void function
>qnorm.c: In function 'using_target_group':
>qnorm.c:1519: warning: control reaches end of non-void function
>qnorm.c: In function 'distribute_group':
>qnorm.c:457: warning: control reaches end of non-void function
>qnorm.c: In function 'normalize_group':
>qnorm.c:452: warning: control reaches end of non-void function
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rlm.c -o rlm.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rlm_anova.c -o rlm_anova.o
>rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects':
>rlm_anova.c:1205: warning: unused variable 'endprobe'
>rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects':
>rlm_anova.c:1378: warning: unused variable 'varderivpsi'
>rlm_anova.c:1378: warning: unused variable 'm'
>rlm_anova.c:1378: warning: unused variable 'vs'
>rlm_anova.c:1371: warning: unused variable 'scale'
>rlm_anova.c:1370: warning: unused variable 'Kappa'
>rlm_anova.c:1369: warning: unused variable 'sumderivpsi'
>rlm_anova.c:1367: warning: unused variable 'sumpsi2'
>rlm_anova.c:1366: warning: unused variable 'k1'
>rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects':
>rlm_anova.c:1457: warning: unused variable 'endprobe'
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rlm_se.c -o rlm_se.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rma_background4.c -o rma_background4.o
>rma_background4.c: In function 'rma_bg_correct':
>rma_background4.c:338: warning: unused variable 'param'
>rma_background4.c:337: warning: unused variable 'j'
>rma_background4.c: In function 'R_rma_bg_correct':
>rma_background4.c:457: warning: unused variable 'j'
>rma_background4.c: In function 'rma_bg_correct_group':
>rma_background4.c:319: warning: control reaches end of non-void function
>rma_background4.c: In function 'R_rma_bg_correct':
>rma_background4.c:456: warning: 'PMcopy' may be used uninitialized in this function
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rma_common.c -o rma_common.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c weightedkerneldensity.c -o weightedkerneldensity.o
>gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -lpthread -lgfortran -lm -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -L/usr/lib64/R/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices ...
>* DONE (preprocessCore)
>+ test -d preprocessCore/src
>+ cd preprocessCore/src
>+ rm -f R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o preprocessCore.so
>+ rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/R.css
>+ install -m 664 -p /builddir/build/SOURCES/preprocessCore_license /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore
>+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/preprocessCore
>extracting debug info from /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/libs/preprocessCore.so
>811 blocks
>+ /usr/lib/rpm/check-buildroot
>+ /usr/lib/rpm/redhat/brp-compress
>+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
>+ /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
>+ /usr/lib/rpm/brp-python-bytecompile
>+ /usr/lib/rpm/redhat/brp-python-hardlink
>+ /usr/lib/rpm/redhat/brp-java-repack-jars
>Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.DfKmL4
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd preprocessCore
>+ unset DISPLAY
>+ /usr/bin/R CMD check preprocessCore
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>=================================
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>Transcript written on pdflatex.log.
>fmtutil: /builddir/.texlive2007/texmf-var/web2c/pdftex/pdflatex.fmt installed.
> OK
>* using log directory '/builddir/build/BUILD/preprocessCore/preprocessCore.Rcheck'
>* using R version 2.10.0 (2009-10-26)
>* using session charset: UTF-8
>* checking for file 'preprocessCore/DESCRIPTION' ... OK
>* this is package 'preprocessCore' version '1.6.0'
>* checking package name space information ... OK
>* checking package dependencies ... OK
>* checking if this is a source package ... OK
>* checking for executable files ... OK
>* checking whether package 'preprocessCore' can be installed ... OK
>* checking package directory ... OK
>* checking for portable file names ... OK
>* checking for sufficient/correct file permissions ... OK
>* checking DESCRIPTION meta-information ... OK
>* checking top-level files ... OK
>* checking index information ... OK
>* checking package subdirectories ... OK
>* checking R files for non-ASCII characters ... OK
>* checking R files for syntax errors ... OK
>* checking whether the package can be loaded ... OK
>* checking whether the package can be loaded with stated dependencies ... OK
>* checking whether the name space can be loaded with stated dependencies ... OK
>* checking for unstated dependencies in R code ... OK
>* checking S3 generic/method consistency ... OK
>* checking replacement functions ... OK
>* checking foreign function calls ... OK
>* checking R code for possible problems ... OK
>* checking Rd files ... NOTE
>prepare_Rd: rcModelPLMd.Rd:35-36: Dropping empty section \seealso
>prepare_Rd: rcModelPLMr.Rd:53-54: Dropping empty section \seealso
>prepare_Rd: rcModels.Rd:42-43: Dropping empty section \seealso
>* checking Rd metadata ... OK
>* checking Rd cross-references ... WARNING
>Warning: unable to access index for repository http://cran.r-project.org/src/contrib
>Warning: unable to access index for repository http://www.omegahat.org/R/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/bioc/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/data/annotation/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/data/experiment/src/contrib
>Unknown package(s) âaffyâ in Rd xrefs
>* checking for missing documentation entries ... OK
>* checking for code/documentation mismatches ... OK
>* checking Rd \usage sections ... OK
>* checking line endings in C/C++/Fortran sources/headers ... OK
>* checking line endings in Makefiles ... OK
>* checking for portable compilation flags in Makevars ... OK
>* checking for portable use of $BLAS_LIBS ... OK
>* checking examples ... OK
>* checking tests ...
>  Running âPLMdtest.Râ
> OK
>* checking PDF version of manual ... OK
>WARNING: There was 1 warning, see
>  /builddir/build/BUILD/preprocessCore/preprocessCore.Rcheck/00check.log
>for details
>+ exit 0
>Processing files: R-preprocessCore-1.6.0-2.fc13.x86_64
>RPM build errors:
>error: File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/latex
>error: File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/man
>error: File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/CONTENTS
>error: File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/R-ex
>    File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/latex
>    File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/man
>    File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/CONTENTS
>    File not found: /builddir/build/BUILDROOT/R-preprocessCore-1.6.0-2.fc13.x86_64/usr/lib64/R/library/preprocessCore/R-ex
>Child returncode was: 1
>EXCEPTION: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec']
>Traceback (most recent call last):
>  File "/usr/lib/python2.6/site-packages/mock/trace_decorator.py", line 70, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python2.6/site-packages/mock/util.py", line 324, in do
>    raise mock.exception.Error, ("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>Error: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-preprocessCore.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 539007: 371093 | 371094 | 371095 | 371096 | 371097 | 371098