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

[gregor herrmann]

On Wed, 14 Dec 2016 08:58:30 +0100, Andreas Tille wrote:

> 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.

The tests started failing on 2016-09-01.
perl 5.24 entered unstable on 23 Sep 2016.

What did happen around the time was the removal of '.' from @INC.

But still, I think the failure is unrelated;
https://ci.debian.net/data/packages/unstable/amd64/v/vcftools/20160901_192825.log
(the first failure) doesn't show any changes in dependencies. But
has perl 5.22.2-4. But re-adding . to @INC in
/etc/perl/sitecustomize.pl doesn't change anything.

The log from the failed test before is:
https://ci.debian.net/data/packages/unstable/amd64/v/vcftools/20160901_164433.log

-tabix 1.3.1-2
+tabix 1.3.1-3

Not sure if and how this is related.


The test call can be shortened to:

# vcf-fix-ploidy -s fix-ploidy.samples < fix-ploidy.vcf | grep 61098
20  61098   .   C   A,T 999 PASS    AC1=41;AF1=0.2104;DP4=209,284,67,76;DP=658;FQ=999;MQ=45;PV4=0.39,4.4e-10,0.0034,0.2 GT:PL:DP:SP:GQ  0/1:0,9,72,5,6,7:3:212:12   0/0:0,15,140,5,6,7:5:458752:18  1:147,0,5:7:384:24  0:0,131,5:5:208:18  0/0:0,9,83,5,6,7:3:392:12   0/0:0,6,56,5,6,7:2:204:9

Which already has the 0/1:0,9,72,5,6,7 sequence which is not the
expected "0 0,9,72,5,6,7". And I don't know what either of them mean
...

And /usr/share/perl5/Vcf.pm has 3523 lines which I'm not going to
read and try to understand now :)


Cheers,
gregor

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