Attachment 370938 Details for Bug 538974 – build.log

build.log

build.log (text/plain), 11.31 KB, created by FTBFS on 2009-11-19 16:17:08 UTC

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Creator: FTBFS

Created: 2009-11-19 16:17:08 UTC

Size: 11.31 KB

patch

obsolete

>Mock Version: 0.9.19
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-GeneR.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-GeneR-2.14.0-2.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1ceb890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-GeneR.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Wrote: /builddir/build/SRPMS/R-GeneR-2.14.0-2.fc13.src.rpm
>Child returncode was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-GeneR.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-GeneR-2.14.0-2.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1ceb890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-GeneR.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.6FZZB6
>+ umask 022
>+ cd /builddir/build/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /builddir/build/BUILD
>+ rm -rf GeneR
>+ /bin/mkdir -p GeneR
>+ cd GeneR
>+ /bin/tar -xf -
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/GeneR_2.14.0.tar.gz
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ echo 'Patch #0 (R-GeneR-gcc44.patch):'
>Patch #0 (R-GeneR-gcc44.patch):
>+ /bin/cat /builddir/build/SOURCES/R-GeneR-gcc44.patch
>+ /usr/bin/patch -s -p0 --fuzz=0
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0o2DaV
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd GeneR
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.OQX3JJ
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64
>++ dirname /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64
>+ cd GeneR
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ rm -rf /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library
>+ R CMD INSTALL GeneR -l /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library
>* installing *source* package 'GeneR' ...
>** libs
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c GeneR_glob.cc -o GeneR_glob.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c GeneR_seq.cc -o GeneR_seq.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c complementaire.cc -o complementaire.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c compoSeq.cc -o compoSeq.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dnaRna.cc -o dnaRna.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c libIndex.cc -o libIndex.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c libStrings.cc -o libStrings.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c makeIndex.cc -o makeIndex.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c masked.cc -o masked.o
>masked.cc: In function 'int masked::lecturefasta(FILE*, char*, int, int)':
>masked.cc:182: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c misc.cc -o misc.o
>misc.cc: In function 'SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)':
>misc.cc:31: warning: 'multiple' may be used uninitialized in this function
>misc.cc:30: warning: 'ans' may be used uninitialized in this function
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readEmblDescript.cc -o readEmblDescript.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readIndex.cc -o readIndex.o
>readIndex.cc: In function 'void sizeseqgbk(char**, int*, char**)':
>readIndex.cc:188: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
>readIndex.cc:199: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readLocation.cc -o readLocation.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readSeqEmbl.cc -o readSeqEmbl.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readSeqFasta.cc -o readSeqFasta.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c readSeqGbk.cc -o readSeqGbk.o
>readSeqGbk.cc: In function 'void ReadSeqGBK(char**, char**, int*, int*, int*, int*, int*)':
>readSeqGbk.cc:165: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c seqManip.cc -o seqManip.o
>gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c strcasestr.c -o strcasestr.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c translate.cc -o translate.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c upperSeq.cc -o upperSeq.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c vecteurs.cc -o vecteurs.o
>g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c writeFasta.cc -o writeFasta.o
>g++ -m64 -shared -L/usr/local/lib64 -o GeneR.so GeneR_glob.o GeneR_seq.o complementaire.o compoSeq.o dnaRna.o libIndex.o libStrings.o makeIndex.o masked.o misc.o readEmblDescript.o readIndex.o readLocation.o readSeqEmbl.o readSeqFasta.o readSeqGbk.o seqManip.o strcasestr.o translate.o upperSeq.o vecteurs.o writeFasta.o -L/usr/lib64/R/lib -lR
>** R
>** demo
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices ...
>* DONE (GeneR)
>+ test -d GeneR/src
>+ cd GeneR/src
>+ rm -f GeneR_glob.o GeneR_seq.o complementaire.o compoSeq.o dnaRna.o libIndex.o libStrings.o makeIndex.o masked.o misc.o readEmblDescript.o readIndex.o readLocation.o readSeqEmbl.o readSeqFasta.o readSeqGbk.o seqManip.o strcasestr.o translate.o upperSeq.o vecteurs.o writeFasta.o GeneR.so
>+ rm -rf /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/R.css
>+ iconv -f iso8859-1 -t utf-8 /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/COPYING
>+ mv -f /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/COPYING.conv /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/COPYING
>+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/GeneR
>extracting debug info from /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/libs/GeneR.so
>276 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.msuNrY
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd GeneR
>+ unset DISPLAY
>+ exit 0
>Processing files: R-GeneR-2.14.0-2.fc13.x86_64
>RPM build errors:
>error: File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/latex
>error: File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/man
>error: File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/CONTENTS
>error: File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/R-ex
>    File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/latex
>    File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/man
>    File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/CONTENTS
>    File not found: /builddir/build/BUILDROOT/R-GeneR-2.14.0-2.fc13.x86_64/usr/lib64/R/library/GeneR/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-GeneR.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-GeneR.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 538974: 370934 | 370935 | 370936 | 370937 | 370938 | 370939