[Debian-med-packaging] Bug#1032557: libvcflib breaks freebayes autopkgtest: Error: signal 11

[Paul Gevers]

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-ci at 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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