Special thanks to the ftpmaster behind the curtain!
libstatgen1 made it through new in just a few days.
----- Forwarded message from Debian Bug Tracking System <owner@bugs.debian.org> -----
Date: Tue, 07 Dec 2021 19:03:21 +0000
From: Debian Bug Tracking System <owner@bugs.debian.org>
To: Étienne Mollier <emollier@debian.org>
Subject: Bug#996409: marked as done (libstatgen breaks minimac4 autopkgtest: Segmentation fault)
X-Mailer: MIME-tools 5.509 (Entity 5.509)
Your message dated Tue, 07 Dec 2021 19:00:17 +0000
with message-id <E1mufhJ-0008tx-I3@fasolo.debian.org>
and subject line Bug#996409: fixed in libstatgen 1.0.15-3~0exp0
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.
(NB: If you are a system administrator and have no idea what this
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--
996409: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996409
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
Date: Wed, 13 Oct 2021 21:26:27 +0200
From: Paul Gevers <elbrus@debian.org>
To: submit@bugs.debian.org
Subject: libstatgen breaks minimac4 autopkgtest: Segmentation fault
User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101
Thunderbird/78.14.0
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-ci@lists.debian.org
User: debian-ci@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
Date: Tue, 07 Dec 2021 19:00:17 +0000
From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
To: 996409-close@bugs.debian.org
Subject: Bug#996409: fixed in libstatgen 1.0.15-3~0exp0
Source: libstatgen
Source-Version: 1.0.15-3~0exp0
Done: Étienne Mollier <emollier@debian.org>
We believe that the bug you reported is fixed in the latest version of
libstatgen, 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 996409@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emollier@debian.org> (supplier of updated libstatgen 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 ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 02 Dec 2021 23:04:37 +0100
Binary: libstatgen-dev libstatgen-doc libstatgen1 libstatgen1-dbgsym
Source: libstatgen
Architecture: all amd64 source
Version: 1.0.15-3~0exp0
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 996409
Description:
libstatgen-dev - development files for the libStatGen
libstatgen-doc - documentation files for the libStatGen
libstatgen1 - processing and analyzing next generation sequencing and genotypin
Changes:
libstatgen (1.0.15-3~0exp0) experimental; urgency=medium
.
* Team upload.
* SONAME bump from libstatgen0 to libstatgen1 (Closes: #996409)
* d/copyright: update years
* Add spelling.patch: fix typos caught by lintian
Checksums-Sha1:
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6e40902fd81c63fe9c8aa6be5aa10ece2bf75a27 1209212 libstatgen-doc_1.0.15-3~0exp0_all.deb
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f2f8e928472f7b67294d710a7fd7b81392c42ff1 316728 libstatgen1_1.0.15-3~0exp0_amd64.deb
4c145b0e120db940b4299ba7bdb7e94820ae477f 7262 libstatgen_1.0.15-3~0exp0_amd64.buildinfo
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Checksums-Sha256:
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Files:
bdab22b65389b6bad205f07a23eb2236 121656 libdevel optional libstatgen-dev_1.0.15-3~0exp0_amd64.deb
88ddaa0c654c5c613f71c9eadf33fd95 1209212 doc optional libstatgen-doc_1.0.15-3~0exp0_all.deb
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03b08fa60982df3ee109c0b7f1bdd2da 20644 science optional libstatgen_1.0.15-3~0exp0.debian.tar.xz
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----- End forwarded message -----
--
Étienne Mollier <emollier@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.
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