Hi Gregor, thanks for your analysis.
On Wed, Dec 14, 2016 at 08:00:00PM +0100, gregor herrmann 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. Ahhh, that's the changelog date from 1.3.1-3 with the following patch included: https://anonscm.debian.org/cgit/debian-med/htslib.git/tree/debian/patches/define_PATH_MAX.patch While there is some time coincicence I can not imagine that this specific patch would be able to cause this result. To be really sure I tried with a tabix where I reverted the patch and there is the same test failure. > 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. I think its a nice hint anyway even if the actual change in this package does not have caused the failed test. I even fetched tabix 1.3.1-2 + libhts1 1.3.1-2 from snapshot.d.o and the test failure remains. > 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 > ... I confirm that I have no idea what this means but it somehow looks "quite similar". I'll ask upstream about this. > And /usr/share/perl5/Vcf.pm has 3523 lines which I'm not going to > read and try to understand now :) How comes? ;-) Thanks for your very helpful analysis Andreas. -- http://fam-tille.de