[Debian-med-packaging] Bug#1000475: minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

[Paul Gevers]

Source: minimac4
Version: 1.0.2-3
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at 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


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