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 -- .''`. https://info.comodo.priv.at/ - Debian Developer https://www.debian.org : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D 85FA BB3A 6801 8649 AA06 `. `' Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe `- NP: Rolling Stones
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