Your message dated Wed, 08 Dec 2021 20:38:52 +0000
with message-id <[email protected]>
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 [email protected] with problems
--- Begin Message ---
Source: minimac4
Version: 1.0.2-3
X-Debbugs-CC: [email protected]
Severity: serious
User: [email protected]
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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: minimac4
Source-Version: 1.0.2-4
Done: Étienne Mollier <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (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 [email protected])
-----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
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1000475
Changes:
minimac4 (1.0.2-4) unstable; urgency=medium
.
* Team upload.
* Rebuild minimac4 against libstatgen1. (Closes: #1000475)
Checksums-Sha1:
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0c4603eba0ce09f7eccd7e132cd5d335d2573ad4 1219564 minimac4_1.0.2-4.debian.tar.xz
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Checksums-Sha256:
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minimac4_1.0.2-4.dsc
3aa1634fe18173389aa4e700bcf72053f27c91d129bd55eb0ba280100c19d004 1219564
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minimac4_1.0.2-4_amd64.buildinfo
Files:
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c694968e736ff8dae360a2523d8029d7 1219564 science optional
minimac4_1.0.2-4.debian.tar.xz
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minimac4_1.0.2-4_amd64.buildinfo
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