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

[Andreas Tille]

Hi,

On Tue, Nov 01, 2016 at 11:05:02AM +0000, Iain Lane wrote:
> 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
> > #     '

Since the bug is menitoning the Perl version bump I wonder whether the
perl team would have an explanation / fix for the issue.

Kind regards

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

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