[Debian-med-packaging] Bug#842794: autopkgtests fail (since perl 5.24?): Failed test 'Testing vcf-fix-ploidy .. cat ...

[Iain Lane]

Package: vcftools
Version: 0.1.14+dfsg-3
Severity: normal

Hi,

I noticed in Ubuntu, where we run autopkgtests as part of britney
migration, that vcftools fails now. You can see on ci.debian.net[0]

> not ok 26 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n'
> #   Failed test 'Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n''
> #   at ./test.t line 452.
> #     Structures begin differing at:
> #          $got->[0] = '61098   M1 0/1 0,9,72,5,6,7     M2 0/0 0,15,140,5,6,7   F3 1 147,0,5    F4 0 0,131,5    M5 0/0 0,9,83,5,6,7     M6 0/0 0,6,56,5,6,7
> #     '
> #     $expected->[0] = '61098   M1 0 0,9,72,5,6,7       M2 0 0,15,140,5,6,7     F3 1/1 147,0,5  F4 0/0 0,131,5  M5 0 0,9,83,5,6,7       M6 0 0,6,56,5,6,7
> #     '

Any ideas?

Cheers,

-- 
Iain Lane                                  [ iain at orangesquash.org.uk ]
Debian Developer                                   [ laney at debian.org ]
Ubuntu Developer                                   [ laney at ubuntu.com ]

[0] https://ci.debian.net/data/packages/unstable/amd64/v/vcftools/20161028_112724.autopkgtest.log.gz