Your message dated Sun, 06 Aug 2023 08:10:11 +0000
with message-id <[email protected]>
and subject line Bug#1032557: fixed in libvcflib 1.0.9+dfsg1-1
has caused the Debian Bug report #1032557,
regarding libvcflib breaks ABI without SONAME bump
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
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--
1032557: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1032557
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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: [email protected]
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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: libvcflib
Source-Version: 1.0.9+dfsg1-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libvcflib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated libvcflib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 23 Jul 2023 10:42:25 +0200
Source: libvcflib
Binary: libvcflib-dev libvcflib-tools libvcflib-tools-dbgsym libvcflib2
libvcflib2-dbgsym
Architecture: source amd64
Version: 1.0.9+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
libvcflib-dev - C++ library for parsing and manipulating VCF files
(development)
libvcflib-tools - C++ library for parsing and manipulating VCF files (tools)
libvcflib2 - C++ library for parsing and manipulating VCF files
Closes: 1032557
Changes:
libvcflib (1.0.9+dfsg1-1) unstable; urgency=medium
.
* Bump SOVERSION due to ABI change
Closes: #1032557
* Attempt to use d-shlibs delayed for later once shared and static lib
are created both
* Drop unneeded header files with questionable licenses
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--- End Message ---
