Your message dated Thu, 09 Mar 2023 10:49:02 +0000
with message-id <e1padpw-006tao...@fasolo.debian.org>
and subject line Bug#1032557: fixed in freebayes 1.3.7-1~exp
has caused the Debian Bug report #1032557,
regarding libvcflib breaks freebayes autopkgtest: Error: signal 11
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 ow...@bugs.debian.org
immediately.)
--
1032557: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1032557
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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: 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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: freebayes
Source-Version: 1.3.7-1~exp
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
freebayes, 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 1032...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated freebayes 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 09 Mar 2023 11:17:58 +0100
Source: freebayes
Architecture: source
Version: 1.3.7-1~exp
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1032557
Changes:
freebayes (1.3.7-1~exp) experimental; urgency=medium
.
[ Nilesh Patra ]
* New upstream version 1.3.7
Closes: #1032557
* Bump Standards-Version to 4.6.2 (no changes needed)
Checksums-Sha1:
3a08578a0bb6610137bfe28ac30698c3d77761d8 2248 freebayes_1.3.7-1~exp.dsc
aa5e76b874f5daa90102152d542fa30f5bac701f 2901909 freebayes_1.3.7.orig.tar.gz
8aaefbb3a7c49bb427a55d0d7467de8375902b4f 11520
freebayes_1.3.7-1~exp.debian.tar.xz
0545f7e413f0bb94b21343428c5952cc11cdcca7 11262
freebayes_1.3.7-1~exp_amd64.buildinfo
Checksums-Sha256:
b2d57d6a90ee878a10ec3a28d31e908668c3f1aee9905c3ec6e3526fd7c2fecf 2248
freebayes_1.3.7-1~exp.dsc
73de20987bfad317099e5bb2f651073351906b9fb1392d704332f401fbfbb5c6 2901909
freebayes_1.3.7.orig.tar.gz
0f519dcc9bf9719da911c72de41ab570fd90b7beb38055300fe40707e0d7fc6b 11520
freebayes_1.3.7-1~exp.debian.tar.xz
949e2fe26bbb7785d74372d8f40a1a4459f9e503677e90268cc94a8e39b35e34 11262
freebayes_1.3.7-1~exp_amd64.buildinfo
Files:
642ccade9d66e64e58ec37cc83eab270 2248 science optional
freebayes_1.3.7-1~exp.dsc
83a9eaef72b98e3c03c287ec73c69687 2901909 science optional
freebayes_1.3.7.orig.tar.gz
23ee4258177f9ae2036b3c3933b3a55e 11520 science optional
freebayes_1.3.7-1~exp.debian.tar.xz
92484bbc7a48dd6cede81f288a6a25cd 11262 science optional
freebayes_1.3.7-1~exp_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=PQrH
-----END PGP SIGNATURE-----
--- End Message ---
