Source: libvcflib, freebayes Control: found -1 libvcflib/1.0.9+dfsg-1 Control: found -1 freebayes/1.3.6-2 Severity: serious Tags: sid bookworm User: debian...@lists.debian.org Usertags: breaks needs-update
Dear maintainer(s),With a recent upload of libvcflib the autopkgtest of freebayes fails in testing when that autopkgtest is run with the binary packages of libvcflib from unstable. It passes when run with only packages from testing. In tabular form:
pass fail libvcflib from testing 1.0.9+dfsg-1 freebayes from testing 1.3.6-2 all others from testing from testing I copied some of the output at the bottom of this report.Currently this regression is blocking the migration of libvcflib to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=libvcflib https://ci.debian.net/data/autopkgtest/testing/amd64/f/freebayes/32031881/log.gz .: README.test_data bash-tap freebayes-env.yaml performance pipeline.sh regression runner.sh snakemake-freebayes-parallel.smk splice t targets.bed test-simple-bash test.alt test.bam test.bam.bai test.bed test.ref test.ref.fai test.vcf tiny ./bash-tap: ./performance: benchmark.md ./regression: NA12878.chr22.tiny.vcf README.md ./splice: 1:883884-887618.bam 1:883884-887618.bam.bai 1:883884-887618.fa 1:883884-887618.fa.fai ./t: 00_region_and_target_handling.t 01_call_variants.t 01b_call_variants.t 02_multi_bam.t 03_reference_bases.t ./test-simple-bash: ./tiny: 1read.bam 1read.bam.bai NA12878.chr22.tiny.bam NA12878.chr22.tiny.bam.bai NA12878.chr22.tiny.cram NA12878.chr22.tiny.giab.vcf NA12878.chr22.tiny.hla.bam NA12878.chr22.tiny.hla.bam.bai hla.fa hla.fa.fai hla.vcf.gz hla.vcf.gz.tbi q with spaces.fa q with spaces.fa.fai q with spaces.regions q.fa q.fa.fai q.regions q.vcf.gz q.vcf.gz.tbi q_spiked.vcf.gz q_spiked.vcf.gz.tbi Test 1 Passed Test 2 Passed Test 3 Passed Test 4 Passed Test 5 Passed Test 6 Passed Test 7 Passed Test 8 Error: signal 11: freebayes(+0xa355a)[0x55743c9a055a] /lib/x86_64-linux-gnu/libc.so.6(+0x3bf90)[0x7fc692924f90] /lib/x86_64-linux-gnu/libvcflib.so.1(_ZN6vcfliblsERSoRNS_7VariantE+0xfa0)[0x7fc692e883e0] freebayes(+0x1247b)[0x55743c90f47b] /lib/x86_64-linux-gnu/libc.so.6(+0x2718a)[0x7fc69291018a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)[0x7fc692910245] freebayes(+0x150d1)[0x55743c9120d1] autopkgtest [13:13:47]: test run-unit-test
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