Your message dated Thu, 11 Nov 2021 11:03:41 +0000
with message-id <e1ml7rp-000ey8...@fasolo.debian.org>
and subject line Bug#996409: fixed in minimac4 1.0.2-3
has caused the Debian Bug report #996409,
regarding libstatgen breaks minimac4 autopkgtest: Segmentation fault
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.
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--
996409: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996409
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: libstatgen, minimac4
Control: found -1 libstatgen/1.0.15-1
Control: found -1 minimac4/1.0.2-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of libstatgen the autopkgtest of minimac4 fails in
testing when that autopkgtest is run with the binary packages of
libstatgen from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
libstatgen from testing 1.0.15-1
minimac4 from testing 1.0.2-2
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 libstatgen 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=libstatgen
https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/15927915/log.gz
autopkgtest [21:29:13]: test run-sample-analysis: [-----------------------
--------------------------------------------------------------------------------
Minimac4 - Fast Imputation Based on State Space Reduction HMM
--------------------------------------------------------------------------------
(c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds
Mary Kate Wing, Goncalo Abecasis
Version: 1.0.2;
Built: 2019-11-05 by Reproducible
Command Line Options:
Reference Haplotypes : --refHaps [refPanel.m3vcf.gz], --passOnly,
--rsid, --referenceEstimates [ON],
--mapFile [docs/geneticMapFile.b38.map.txt.gz]
Target Haplotypes : --haps [targetStudy.vcf.gz]
Output Parameters : --prefix [testRun], --estimate, --nobgzip,
--vcfBuffer [200], --format [GT,DS],
--allTypedSites, --meta, --memUsage
Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb
[3.00]
Subset Parameters : --chr [], --start, --end, --window
Approximation Parameters : --minimac3, --probThreshold [0.01],
--diffThreshold [0.01], --topThreshold [0.01]
Other Parameters : --log, --help, --cpus [5], --params
PhoneHome : --noPhoneHome [ON], --phoneHomeThinning [50]
URL = http://genome.sph.umich.edu/wiki/Minimac4
Starting Main Imputation/Estimation Analysis ...
Performing preliminary check on input parameters...
------------------------------------------------------------------------------
PRELIMINARY FILE CHECK
------------------------------------------------------------------------------
Checking GWAS haplotype file : targetStudy.vcf.gz
Gathering variant information ...
Segmentation fault
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: minimac4
Source-Version: 1.0.2-3
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
minimac4, 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 996...@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 minimac4 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, 11 Nov 2021 11:48:01 +0100
Source: minimac4
Architecture: source
Version: 1.0.2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 996409
Changes:
minimac4 (1.0.2-3) unstable; urgency=medium
.
* Team upload.
* Rebuild minimac4 against new version of libstatgen
Closes: #996409
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Remove obsolete fields Contact, Name from debian/upstream/metadata (already
present in machine-readable debian/copyright).
* watch file standard 4 (routine-update)
Checksums-Sha1:
44690f6d9401d672e33bb7a92a329b86d39161a3 2008 minimac4_1.0.2-3.dsc
dfe989e13b57eee2c5528fed63ccf5e908c5b6e5 1219656 minimac4_1.0.2-3.debian.tar.xz
35dc54d7d7fb5d5bb647a5b22d46170c8eb6e74a 6923 minimac4_1.0.2-3_amd64.buildinfo
Checksums-Sha256:
187661efe8e5b8f0252847712a9f5935630c5c12a8ac097a637407a231495833 2008
minimac4_1.0.2-3.dsc
e5dd769e838782f13dc8f93a2d7268fa76d8cfe285f97e22160b7b8c92781009 1219656
minimac4_1.0.2-3.debian.tar.xz
9af32719b6457fe4afb42f7d577ffb0770dd31e333c18774e7b0d19c0a6748b3 6923
minimac4_1.0.2-3_amd64.buildinfo
Files:
72e5ab4a64aeec87a07f9f9be253cb6e 2008 science optional minimac4_1.0.2-3.dsc
a27235c3aabac0f3770b67b5699fe1a4 1219656 science optional
minimac4_1.0.2-3.debian.tar.xz
7db2a5e3ada81fb63b8959ab168d9fd4 6923 science optional
minimac4_1.0.2-3_amd64.buildinfo
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--- End Message ---
