[Debian-med-packaging] Bug#1000782: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

[Andreas Tille]

Control: reopen -1
Control: tags -1 confirmed
Control: tags -1 upstream
Control: forwarded -1 Christopher Chang <chrchang at alumni.caltech.edu>

Hi Christopher (and Dylan),

I verified the latest version (29 Jan 2022) of plink2 with the same
result for the CI test we are doing in Debian (which was written by
Dylan):

$ plink2 --dummy 33 65537 0.1 dosage-freq=0.1 --out tmp_data
PLINK v2.00a3 SSE4.2 (29 Jan 2022)             www.cog-genomics.org/plink/2.0/
(C) 2005-2022 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: Thu Feb 17 06:34:30 2022
31998 MiB RAM detected; reserving 15999 MiB for main workspace.
Using up to 4 compute threads.
Dummy data (33 samples, 65537 SNPs) written to tmp_data.pgen + tmp_data.pvar +
tmp_data.psam .
End time: Thu Feb 17 06:34:30 2022
/usr/bin/plink2: line 8:   156 Segmentation fault      "${cmd}" "$@"


Please note that for the build the Debian packaged zstd and libdeflate
are used.  This is the same result as for the version released at 11 Oct
2021 which is currently uploaded to Debian unstable.  There is a full
log of the CI test available[1].

Kind regards

      Andreas.


[1] https://ci.debian.net/data/autopkgtest/testing/amd64/p/plink2/19288881/log.gz


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