Your message dated Sun, 21 Jun 2020 19:36:17 +0300 with message-id <20200621163617.GA12137@localhost> and subject line Re: Bug#829741: pbbam: FTBFS (32-bit): pbmerge assertion failure has caused the Debian Bug report #829741, regarding pbbam: FTBFS (32-bit): pbmerge assertion failure to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 829741: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=829741 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: pbbam Version: 0.5.0-1 Severity: serious Justification: fails to build from source (but built successfully in the past) Builds of pbbam for 32-bit architectures such as i386 fail because pbmerge hits an assertion failure in the context of the pbmerge_aligned_ordering and pbmerge_fofn tests, per the excerpted log output below. Could you please take a look? Thanks! TESTDIR=tests/src/cram cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: failed --- tests/src/cram/pbmerge_aligned_ordering.deb.t +++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err @@ -122,35 +122,13 @@ Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2 + pbmerge: /«PKGBUILDDIR»/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed. + Aborted + [134] $ samtools view -H $MERGED_BAM - @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) - @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) - @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) - @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) - @PG\tID:pbmerge-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc) $ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20 - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) [...] - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc) $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Found tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: failed --- tests/src/cram/pbmerge_fofn.deb.t +++ tests/src/cram/pbmerge_fofn.deb.t.err @@ -53,6 +53,9 @@ Normal Merge from FOFN: $ $PBMERGE -o $MERGED_BAM $INPUT_FOFN + pbmerge: /«PKGBUILDDIR»/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed. + Aborted + [134] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" Found @@ -61,33 +64,8 @@ Found $ samtools view -H $MERGED_BAM - @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) - @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) - @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) - @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) - @PG\tID:pbmerge-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc) $ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20 - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) [...] - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc) $ rm $MERGED_BAM $ rm $MERGED_BAM_PBI tests/src/cram/pbmerge_dataset.deb.t: passed # Ran 7 tests, 0 skipped, 2 failed. debian/rules:25: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules:10: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
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--- Begin Message ---On Tue, Jul 05, 2016 at 01:39:45PM -0400, Aaron M. Ucko wrote: >... > Builds of pbbam for 32-bit architectures such as i386 fail because > pbmerge hits an assertion failure in the context of the > pbmerge_aligned_ordering and pbmerge_fofn tests, per the excerpted log > output below. >... This is "fixed"/irrelavant now that the build dependency pbcopper has stopped supporting 32bit. cu Adrian
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