Attachment 420788 Details for Bug 599990 – build.log

build.log

build.log (text/plain), 26.17 KB, created by FTBFS on 2010-06-03 21:12:53 UTC

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Creator: FTBFS

Created: 2010-06-03 21:12:53 UTC

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patch

obsolete

>Mock Version: 1.1.1
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/R-Biostrings.spec'], False, '/var/lib/mock/fedora-development-i386-R-Biostrings-2.14.12-1.fc14.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0xad0b50>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/R-Biostrings.spec']
>Building target platforms: i686
>Building for target i686
>Wrote: /builddir/build/SRPMS/R-Biostrings-2.14.12-1.fc14.src.rpm
>Child returncode was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/R-Biostrings.spec'], False, '/var/lib/mock/fedora-development-i386-R-Biostrings-2.14.12-1.fc14.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0xad0b50>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/R-Biostrings.spec']
>Building target platforms: i686
>Building for target i686
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.kZprzL
>+ umask 022
>+ cd /builddir/build/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /builddir/build/BUILD
>+ rm -rf Biostrings
>+ /bin/mkdir -p Biostrings
>+ cd Biostrings
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/Biostrings_2.14.12.tar.gz
>+ /bin/tar -xf -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.E6odWv
>+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ exit 0
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd Biostrings
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.bIfCkg
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386
>++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386
>+ cd Biostrings
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386
>+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386/usr/lib/R/library
>+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386/usr/lib/R/library
>* installing *source* package 'Biostrings' ...
>** libs
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c BAB_class.c -o BAB_class.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c BitMatrix.c -o BitMatrix.o
>BitMatrix.c: In function 'debug_BitMatrix':
>BitMatrix.c:382: warning: left shift count >= width of type
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c IRanges_stubs.c -o IRanges_stubs.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c MIndex_class.c -o MIndex_class.o
>MIndex_class.c: In function 'SparseMIndex_endIndex':
>MIndex_class.c:192: warning: unused variable 'poffsets_order'
>MIndex_class.c: In function '_get_cachedMIndex_elt':
>MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c PreprocessedTB_class.c -o PreprocessedTB_class.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c R_init_Biostrings.c -o R_init_Biostrings.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c RoSeqs_utils.c -o RoSeqs_utils.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c SparseList_utils.c -o SparseList_utils.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c XStringSet_class.c -o XStringSet_class.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c XStringSet_io.c -o XStringSet_io.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c XString_class.c -o XString_class.o
>XString_class.c:116: warning: 'new_RoSeqs_from_XString' defined but not used
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c align_needwunsQS.c -o align_needwunsQS.o
>align_needwunsQS.c: In function 'align_needwunsQS':
>align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
>align_needwunsQS.c:26: note: 'sc' was declared here
>align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
>align_needwunsQS.c:39: note: 'lkup_val' was declared here
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c align_utils.c -o align_utils.o
>align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
>align_utils.c:225: warning: 'indelStartPattern' may be used uninitialized in this function
>align_utils.c:225: warning: 'indelWidthPattern' may be used uninitialized in this function
>align_utils.c:225: warning: 'indelStartSubject' may be used uninitialized in this function
>align_utils.c:225: warning: 'indelWidthSubject' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c extract_transcripts.c -o extract_transcripts.o
>extract_transcripts.c: In function 'tlocs2rlocs':
>extract_transcripts.c:224: warning: 'nlocs' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c find_palindromes.c -o find_palindromes.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c gtestsim.c -o gtestsim.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c inject_code.c -o inject_code.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c letter_frequency.c -o letter_frequency.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c lowlevel_matching.c -o lowlevel_matching.o
>lowlevel_matching.c: In function '_nedit_for_Proffset':
>lowlevel_matching.c:285: warning: unused variable 'Pc'
>lowlevel_matching.c:284: warning: unused variable 'j'
>lowlevel_matching.c:284: warning: unused variable 'jmin'
>lowlevel_matching.c:284: warning: unused variable 'iplus1'
>lowlevel_matching.c:284: warning: unused variable 'i'
>lowlevel_matching.c:284: warning: unused variable 'b'
>lowlevel_matching.c:284: warning: unused variable 'B'
>lowlevel_matching.c:283: warning: unused variable 'row_length'
>lowlevel_matching.c:283: warning: unused variable 'curr_row'
>lowlevel_matching.c:283: warning: unused variable 'prev_row'
>lowlevel_matching.c:283: warning: unused variable 'max_nedit_plus1'
>lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
>lowlevel_matching.c:485: warning: 'ans_elt' may be used uninitialized in this function
>lowlevel_matching.c:485: warning: 'ans_nrow' may be used uninitialized in this function
>lowlevel_matching.c:486: warning: 'ans' may be used uninitialized in this function
>lowlevel_matching.c: In function 'XString_match_pattern_at':
>lowlevel_matching.c:437: warning: 'ans_elt' may be used uninitialized in this function
>lowlevel_matching.c:438: warning: 'ans' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_BOC.c -o match_BOC.o
>match_BOC.c: In function 'BOC_exact_search':
>match_BOC.c:331: warning: label 'continue0' defined but not used
>match_BOC.c:268: warning: unused variable 'noffsets'
>match_BOC.c:268: warning: unused variable 'offsets'
>match_BOC.c:268: warning: unused variable 'j'
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_BOC2.c -o match_BOC2.o
>match_BOC2.c: In function 'BOC2_exact_search':
>match_BOC2.c:288: warning: label 'continue0' defined but not used
>match_BOC2.c:234: warning: unused variable 'noffsets'
>match_BOC2.c:234: warning: unused variable 'offsets'
>match_BOC2.c:234: warning: unused variable 'j'
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_PWM.c -o match_PWM.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_WCP.c -o match_WCP.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pattern.c -o match_pattern.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
>match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
>match_pattern_boyermoore.c:399: warning: 'i1' may be used uninitialized in this function
>match_pattern_boyermoore.c:399: warning: 'i2' may be used uninitialized in this function
>match_pattern_boyermoore.c:399: warning: 'j1' may be used uninitialized in this function
>match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pattern_indels.c -o match_pattern_indels.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pattern_shiftor.c -o match_pattern_shiftor.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pdict.c -o match_pdict.o
>match_pdict.c: In function 'XStringSet_vmatch_pdict':
>match_pdict.c:320: warning: 'ans' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pdict_ACtree.c -o match_pdict_ACtree.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
>match_pdict_ACtree2.c:592: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pdict_Twobit.c -o match_pdict_Twobit.o
>match_pdict_Twobit.c: In function 'build_Twobit':
>match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_pdict_utils.c -o match_pdict_utils.o
>match_pdict_utils.c: In function 'match_ppheadtail0':
>match_pdict_utils.c:836: warning: unused variable 'ncol'
>match_pdict_utils.c: In function '_match_pdict_all_flanks':
>match_pdict_utils.c:989: warning: unused variable 'subtotal_NFC'
>match_pdict_utils.c:989: warning: unused variable 'total_NFC'
>match_pdict_utils.c:988: warning: unused variable 'NFC'
>match_pdict_utils.c:988: warning: unused variable 'nloci'
>match_pdict_utils.c:988: warning: unused variable 'ndup'
>match_pdict_utils.c: At top level:
>match_pdict_utils.c:460: warning: 'match_headtail_by_loc' defined but not used
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c match_reporting.c -o match_reporting.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c matchprobes.c -o matchprobes.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c pmatchPattern.c -o pmatchPattern.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c replace_letter_at.c -o replace_letter_at.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c strutils.c -o strutils.o
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c utils.c -o utils.o
>utils.c: In function '_get_twobit_signature_at':
>utils.c:240: warning: 'twobit_sign' may be used uninitialized in this function
>utils.c: In function '_get_twobit_signature':
>utils.c:226: warning: 'twobit_sign' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include -I"/usr/lib/R/library/IRanges/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c xscat.c -o xscat.o
>xscat.c: In function 'XStringSet_xscat':
>xscat.c:86: warning: 'ans_length' may be used uninitialized in this function
>xscat.c:63: warning: 'ans_xsbaseclassname' may be used uninitialized in this function
>xscat.c: In function 'XString_xscat':
>xscat.c:36: warning: 'ans_classname' may be used uninitialized in this function
>xscat.c:36: warning: 'ans_length' may be used uninitialized in this function
>gcc -m32 -std=gnu99 -shared -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o extract_transcripts.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_WCP.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o xscat.o -L/usr/lib/R/lib -lR
>installing to /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386/usr/lib/R/library/Biostrings/libs
>** R
>** data
>** inst
>** preparing package for lazy loading
>Attaching package: 'IRanges'
>The following object(s) are masked from 'package:base':
>    Map, cbind, mapply, order, pmax, pmax.int, pmin, pmin.int, rbind,
>    rep.int, table
>in method for 'XString' with signature '"AsIs"': no definition for class "AsIs"
>in method for 'XStringSet' with signature '"AsIs"': no definition for class "AsIs"
>in method for 'XStringSet' with signature '"probetable"': no definition for class "probetable"
>Creating a new generic function for "setequal" in "Biostrings"
>Creating a new generic function for "is.unsorted" in "Biostrings"
>in method for 'BStringViews' with signature '"file"': no definition for class "file"
>in method for 'consensusString' with signature '"BStringViews"': no definition for class "BStringViews"
>in method for 'consensusString' with signature '"DNAStringViews"': no definition for class "DNAStringViews"
>in method for 'consensusString' with signature '"RNAStringViews"': no definition for class "RNAStringViews"
>Creating a new generic function for "ls" in "Biostrings"
>in method for 'PDict' with signature '"AsIs"': no definition for class "AsIs"
>in method for 'PDict' with signature '"probetable"': no definition for class "probetable"
>** help
>*** installing help indices
>  converting help for package 'Biostrings'
>    finding HTML links ... done
>    AAString-class                          html  
>    AMINO_ACID_CODE                         html  
>    AlignedXStringSet-class                 html  
>    BOC_SubjectString-class                 html  
>    Biostrings-internals                    html  
>    DNAString-class                         html  
>    GENETIC_CODE                            html  
>    HNF4alpha                               html  
>    IUPAC_CODE_MAP                          html  
>    InDel-class                             html  
>    MIndex-class                            html  
>    MaskedXString-class                     html  
>    PDict-class                             html  
>    PairwiseAlignedXStringSet-class         html  
>    QualityScaledXStringSet-class           html  
>    RNAString-class                         html  
>    WCP                                     html  
>    XKeySortedData                          html  
>    XKeySortedDataList                      html  
>    XString-class                           html  
>    XStringPartialMatches-class             html  
>    XStringQuality-class                    html  
>    XStringSet-class                        html  
>    XStringSet-io                           html  
>    XStringSetList-class                    html  
>    XStringViews-class                      html  
>    XStringViews-constructors               html  
>    align-utils                             html  
>    basecontent                             html  
>    chartr                                  html  
>    complementSeq                           html  
>    dinucleotideFrequencyTest               html  
>    extractTranscripts                      html  
>Rd warning: ./man/extractTranscripts.Rd:41: missing file link 'IntegerList'
>    findPalindromes                         html  
>    gregexpr2                               html  
>    injectHardMask                          html  
>    letter                                  html  
>    letterFrequency                         html  
>    longestConsecutive                      html  
>    lowlevel-matching                       html  
>    maskMotif                               html  
>    match-utils                             html  
>    matchLRPatterns                         html  
>    matchPDict-exact                        html  
>    matchPDict-inexact                      html  
>    matchPWM                                html  
>    matchPattern                            html  
>    matchProbePair                          html  
>    matchWCP                                html  
>    matchprobes                             html  
>    misc                                    html  
>    needwunsQS                              html  
>    nucleotideFrequency                     html  
>    pairwiseAlignment                       html  
>    phiX174Phage                            html  
>    pid                                     html  
>    pmatchPattern                           html  
>    readFASTA                               html  
>    replaceLetterAt                         html  
>    reverse                                 html  
>    reverseSeq                              html  
>    stringDist                              html  
>    subXString                              html  
>    substitution_matrices                   html  
>    toComplex                               html  
>    translate                               html  
>    trimLRPatterns                          html  
>    xscat                                   html  
>    yeastSEQCHR1                            html  
>** building package indices ...
>** testing if installed package can be loaded
>Error in sub("([^-]+)_.*", "\\1", info$pkgname) : 
>  could not find symbol "extended" in environment of the generic function
>Error : unable to load R code in package 'Biostrings'
>ERROR: loading failed
>* removing '/builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.i386/usr/lib/R/library/Biostrings'
>RPM build errors:
>error: Bad exit status from /var/tmp/rpm-tmp.bIfCkg (%install)
>    Bad exit status from /var/tmp/rpm-tmp.bIfCkg (%install)
>Child returncode was: 1
>EXCEPTION: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/R-Biostrings.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 333, 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 i686 --nodeps builddir/build/SPECS/R-Biostrings.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 599990: 420787 | 420788 | 420789 | 420790 | 420791 | 420792