Attachment 370714 Details for Bug 538932 – build.log

build.log

build.log (text/plain), 21.43 KB, created by FTBFS on 2009-11-19 16:05:51 UTC

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Creator: FTBFS

Created: 2009-11-19 16:05:51 UTC

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patch

obsolete

>Mock Version: 0.9.19
>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-2.12.9-1.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0xcd8890>)
>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-2.12.9-1.fc13.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-2.12.9-1.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0xcd8890>)
>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.iVuiRD
>+ 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_2.12.9.tar.gz
>+ /bin/tar -xf -
>+ 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.weYtmK
>+ 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.ISGySQ
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64
>++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64
>+ cd Biostrings
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library
>+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.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 Dups_utils.c -o Dups_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 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_utils.c -o MIndex_utils.o
>MIndex_utils.c: In function 'SparseMIndex_endIndex':
>MIndex_utils.c:220: warning: unused variable 'poffsets_order'
>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 RoSeq_utils.c -o RoSeq_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 XString_class.c -o XString_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 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
>align_pairwiseAlignment.c: In function 'pairwiseAlignment':
>align_pairwiseAlignment.c:132: warning: unused variable 'prevMinus1'
>align_pairwiseAlignment.c:132: warning: unused variable 'prev'
>align_pairwiseAlignment.c:132: warning: unused variable 'currMinus1'
>align_pairwiseAlignment.c:132: warning: unused variable 'curr'
>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 char_translate.c -o char_translate.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 copy_seq.c -o copy_seq.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 fasta_io.c -o fasta_io.o
>fasta_io.c:101: warning: 'add_desc_LENGTHONLY' defined but not used
>fasta_io.c:136: warning: 'add_empty_seq_CHARAEAE' defined but not used
>fasta_io.c:142: warning: 'append_to_last_seq_CHARAEAE' defined but not used
>fasta_io.c:156: warning: 'add_desc1' 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 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 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 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_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_at.c -o match_pattern_at.o
>match_pattern_at.c: In function '_nedit_for_Proffset':
>match_pattern_at.c:292: warning: unused variable 'Pc'
>match_pattern_at.c:291: warning: unused variable 'j'
>match_pattern_at.c:291: warning: unused variable 'jmin'
>match_pattern_at.c:291: warning: unused variable 'iplus1'
>match_pattern_at.c:291: warning: unused variable 'i'
>match_pattern_at.c:291: warning: unused variable 'b'
>match_pattern_at.c:291: warning: unused variable 'B'
>match_pattern_at.c:290: warning: unused variable 'row_length'
>match_pattern_at.c:290: warning: unused variable 'curr_row'
>match_pattern_at.c:290: warning: unused variable 'prev_row'
>match_pattern_at.c:290: warning: unused variable 'max_nedit_plus1'
>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:373: warning: 'i1' may be used uninitialized in this function
>match_pattern_boyermoore.c:373: warning: 'i2' may be used uninitialized in this function
>match_pattern_boyermoore.c:373: warning: 'j1' may be used uninitialized in this function
>match_pattern_boyermoore.c:374: 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
>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_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:239: warning: 'twobit_sign' may be used uninitialized in this function
>utils.c: In function '_get_twobit_signature':
>utils.c:225: 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:62: warning: 'ans_classname' may be used uninitialized in this function
>xscat.c:62: warning: 'ans_baseClass' 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 Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.o letter_frequency.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_at.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_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o xscat.o -L/usr/lib64/R/lib -lR
>** R
>** data
>** inst
>** preparing package for lazy loading
>Warning: package 'IRanges' was built under R version 2.9.1 and help may not work correctly
>Attaching package: 'IRanges'
>	The following object(s) are masked from package:base :
>	 cbind,
>	 duplicated,
>	 order,
>	 pmax,
>	 pmax.int,
>	 pmin,
>	 pmin.int,
>	 rank,
>	 rbind,
>	 rep.int,
>	 sapply,
>	 sort,
>	 table,
>	 unique 
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "XString" no definition for class: "AsIs"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "XStringSet" no definition for class: "AsIs"
>Creating a new generic function for "setequal" in "Biostrings"
>Creating a new generic function for "match" in "Biostrings"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "BStringViews" no definition for class: "file"
>Creating a new generic function for "ls" in "Biostrings"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "PDict" no definition for class: "AsIs"
>** help
>*** installing help indices
>** building package indices ...
>* DONE (Biostrings)
>+ test -d Biostrings/src
>+ cd Biostrings/src
>+ rm -f BAB_class.o Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.o letter_frequency.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_at.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_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o xscat.o Biostrings.so
>+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/R.css
>+ rm -f /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/doc/GenomeSearching.R
>+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/Biostrings
>extracting debug info from /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/libs/Biostrings.so
>699 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.s4PgBY
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd Biostrings
>+ unset DISPLAY
>+ exit 0
>Processing files: R-Biostrings-2.12.9-1.fc13.x86_64
>RPM build errors:
>error: File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/latex
>error: File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/man
>error: File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/R-ex
>error: File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/CONTENTS
>    File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/latex
>    File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/man
>    File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/R-ex
>    File not found: /builddir/build/BUILDROOT/R-Biostrings-2.12.9-1.fc13.x86_64/usr/lib64/R/library/Biostrings/CONTENTS
>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 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-Biostrings.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 538932: 370710 | 370711 | 370712 | 370713 | 370714 | 370715