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Bug#1000782: plink2: autopkgtest regression: Segmentation fault

Source: plink2
Version: 2.00~a3-211011+dfsg-1
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 plink2 the autopkgtest of plink2 fails in testing when that autopkgtest is run with the binary packages of plink2 from unstable. It passes when run with only packages from testing. In tabular form:

                       pass            fail
plink2                 from testing    2.00~a3-211011+dfsg-1
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 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=plink2


PLINK v2.00a3 SSE4.2 (11 Oct 2021) www.cog-genomics.org/plink/2.0/ (C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to tmp_data.log.
Options in effect:
  --dummy 33 65537 0.1 dosage-freq=0.1
  --out tmp_data

Start time: Sun Nov 28 11:11:17 2021
257840 MiB RAM detected; reserving 128920 MiB for main workspace.
Using up to 48 threads (change this with --threads).

--dummy: 65k variants written.
Dummy data (33 samples, 65537 SNPs) written to tmp_data.pgen + tmp_data.pvar +
tmp_data.psam .
End time: Sun Nov 28 11:11:17 2021
/usr/bin/plink2: line 8:  1566 Segmentation fault      "${cmd}" "$@"
autopkgtest [11:11:17]: test run-sample-analysis

Attachment: OpenPGP_signature
Description: OpenPGP digital signature

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