[Debian-med-packaging] Bug#996409: libstatgen breaks minimac4 autopkgtest: Segmentation fault

[Paul Gevers]

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 at lists.debian.org
User: debian-ci at 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

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