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Red Hat Bugzilla – Attachment 420791 Details for
Bug 599990
FTBFS R-Biostrings-2.14.12-1.fc14
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build.log
build.log (text/plain), 24.71 KB, created by
FTBFS
on 2010-06-03 21:12:57 UTC
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Description:
build.log
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MIME Type:
Creator:
FTBFS
Created:
2010-06-03 21:12:57 UTC
Size:
24.71 KB
patch
obsolete
>Mock Version: 1.1.1 >ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-Biostrings.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-Biostrings-2.14.12-1.fc14.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1a34b10>) >Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-Biostrings.spec'] >Building target platforms: x86_64 >Building for target x86_64 >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 x86_64 --nodeps builddir/build/SPECS/R-Biostrings.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-Biostrings-2.14.12-1.fc14.src.rpm/root/', None, 25200, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x1a34b10>) >Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-Biostrings.spec'] >Building target platforms: x86_64 >Building for target x86_64 >Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Pqsd3m >+ 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 >+ /bin/tar -xf - >+ /usr/bin/gzip -dc /builddir/build/SOURCES/Biostrings_2.14.12.tar.gz >+ STATUS=0 >+ '[' 0 -ne 0 ']' >+ /bin/chmod -Rf a+rX,u+w,g-w,o-w . >+ exit 0 >Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.myt9fF >+ 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.TBxmvX >+ umask 022 >+ cd /builddir/build/BUILD >+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64 '!=' / ']' >+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64 >++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64 >+ mkdir -p /builddir/build/BUILDROOT >+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64 >+ cd Biostrings >+ LANG=C >+ export LANG >+ unset DISPLAY >+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64 >+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64/usr/lib64/R/library >+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64/usr/lib64/R/library >* installing *source* package 'Biostrings' ... >** libs >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c BAB_class.c -o BAB_class.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c BitMatrix.c -o BitMatrix.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c PreprocessedTB_class.c -o PreprocessedTB_class.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_init_Biostrings.c -o R_init_Biostrings.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RoSeqs_utils.c -o RoSeqs_utils.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c SparseList_utils.c -o SparseList_utils.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c XStringSet_class.c -o XStringSet_class.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c XStringSet_io.c -o XStringSet_io.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c XString_class.c -o XString_class.o >XString_class.c:116: warning: 'new_RoSeqs_from_XString' defined but not used >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c find_palindromes.c -o find_palindromes.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c gtestsim.c -o gtestsim.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c inject_code.c -o inject_code.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c letter_frequency.c -o letter_frequency.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_PWM.c -o match_PWM.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_WCP.c -o match_WCP.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_pattern.c -o match_pattern.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_pattern_indels.c -o match_pattern_indels.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_pattern_shiftor.c -o match_pattern_shiftor.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_pdict_ACtree.c -o match_pdict_ACtree.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c match_reporting.c -o match_reporting.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c matchprobes.c -o matchprobes.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c pmatchPattern.c -o pmatchPattern.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c replace_letter_at.c -o replace_letter_at.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c strutils.c -o strutils.o >gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/usr/lib64/R/library/IRanges/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -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 -m64 -std=gnu99 -shared -L/usr/local/lib64 -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/lib64/R/lib -lR >installing to /builddir/build/BUILDROOT/R-Biostrings-2.14.12-1.fc14.x86_64/usr/lib64/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.x86_64/usr/lib64/R/library/Biostrings' >RPM build errors: >error: Bad exit status from /var/tmp/rpm-tmp.TBxmvX (%install) > Bad exit status from /var/tmp/rpm-tmp.TBxmvX (%install) >Child returncode was: 1 >EXCEPTION: Command failed. See logs for output. > # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --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 x86_64 --nodeps builddir/build/SPECS/R-Biostrings.spec'] >LEAVE do --> EXCEPTION RAISED >
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