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

[Niko Tyni]

On Wed, Dec 14, 2016 at 08:00:00PM +0100, gregor herrmann wrote:
> 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
> > > > #     '

> 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.

That's indeed what caused the regression.

> 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

You missed the '-p' parameter above, which makes all the difference.
It's loading Perl code from the specified file with 'do', which no longer
looks in cwd. The load fails silently and the program continues on with
wrong results.

Patch attached.
-- 
Niko Tyni   ntyni at debian.org
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch
Type: text/x-diff
Size: 1589 bytes
Desc: not available
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20161215/bd8d6b8d/attachment.patch>