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