let's make it count
----- Forwarded message from Debian Bug Tracking System <owner@bugs.debian.org> -----
Date: Wed, 08 Dec 2021 20:42:05 +0000
From: Debian Bug Tracking System <owner@bugs.debian.org>
To: Étienne Mollier <emollier@debian.org>
Subject: Bug#1000475: marked as done (minimac4: autopkgtest regression: *** stack smashing detected ***: terminated)
X-Mailer: MIME-tools 5.509 (Entity 5.509)
Your message dated Wed, 08 Dec 2021 20:38:52 +0000
with message-id <E1mv3iG-000Cny-3I@fasolo.debian.org>
and subject line Bug#1000475: fixed in minimac4 1.0.2-4
has caused the Debian Bug report #1000475,
regarding minimac4: autopkgtest regression: *** stack smashing detected ***: terminated
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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--
1000475: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1000475
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
Date: Tue, 23 Nov 2021 21:41:25 +0100
From: Paul Gevers <elbrus@debian.org>
To: submit@bugs.debian.org
Subject: minimac4: autopkgtest regression: *** stack smashing detected ***:
terminated
User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101
Thunderbird/78.14.0
Source: minimac4
Version: 1.0.2-3
X-Debbugs-CC: debian-ci@lists.debian.org
Severity: serious
User: debian-ci@lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing
when that autopkgtest is run with the binary packages of minimac4 from
unstable. It passes when run with only packages from testing. In tabular form:
pass fail
minimac4 from testing 1.0.2-3
all others from testing from testing
I copied some of the output at the bottom of this report. Similar to bug
#1000413 I think this issue points at ABI breakage. The following in the
changelog looks very suspicious:
* Rebuild minimac4 against new version of libstatgen
This is a hint. The test passes in unstable.
Currently this regression is blocking the migration to testing [1]. Can you
please investigate the situation and fix it?
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=minimac4
https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/16920779/log.gz
--------------------------------------------------------------------------------
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: 2021-11-11 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 ...
ERROR !!! Empty Value for Individual : TA98 at First Marker Most probably
a corrupted VCF file. Please check input VCF file !!! *** stack smashing
detected ***: terminated
Aborted
autopkgtest [07:10:54]: test run-sample-analysis
Date: Wed, 08 Dec 2021 20:38:52 +0000
From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
To: 1000475-close@bugs.debian.org
Subject: Bug#1000475: fixed in minimac4 1.0.2-4
Source: minimac4
Source-Version: 1.0.2-4
Done: Étienne Mollier <emollier@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 1000475@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 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 ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 08 Dec 2021 20:37:16 +0100
Source: minimac4
Architecture: source
Version: 1.0.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1000475
Changes:
minimac4 (1.0.2-4) unstable; urgency=medium
.
* Team upload.
* Rebuild minimac4 against libstatgen1. (Closes: #1000475)
Checksums-Sha1:
9fd704e418fc359bd96c27f0d390432a16e0ec27 2012 minimac4_1.0.2-4.dsc
0c4603eba0ce09f7eccd7e132cd5d335d2573ad4 1219564 minimac4_1.0.2-4.debian.tar.xz
06f846df3a7bc4b0050f591aa2140ef2b0f3784a 6713 minimac4_1.0.2-4_amd64.buildinfo
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3aa1634fe18173389aa4e700bcf72053f27c91d129bd55eb0ba280100c19d004 1219564 minimac4_1.0.2-4.debian.tar.xz
c5f465a2dffde08662e7ef37d0b8c24b1f75ea129545a0145581e59f0e83dfc7 6713 minimac4_1.0.2-4_amd64.buildinfo
Files:
63dba25947ddc643df213e48c7c7fb64 2012 science optional minimac4_1.0.2-4.dsc
c694968e736ff8dae360a2523d8029d7 1219564 science optional minimac4_1.0.2-4.debian.tar.xz
949265c72d51886d9f5667bb8249bef3 6713 science optional minimac4_1.0.2-4_amd64.buildinfo
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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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