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Bug#1000475: minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

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


[1] https://qa.debian.org/excuses.php?package=minimac4


-------------------------------------------------------------------------------- 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...


 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
autopkgtest [07:10:54]: test run-sample-analysis

Attachment: OpenPGP_signature
Description: OpenPGP digital signature

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