Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly
On Wed, Dec 12, 2018 at 11:56:28AM +0100, Andreas Tille wrote: > besides the remaining build issues on some architectures there > is a new bug report about random failures. > > I hope you will have a clue about this. They all seem to be the same cause, which I haven't investigated yet. One solution is just to give up with auto-generating data and bundle a larger corpus of test data. The problem comes from the auto-generation step producing files of differing length. I hard coded the random number generator and also put the test system into serial mode so it cannot attempt to run multiple data generation steps in parallel, but it hasn't cured it. A simple method is probably the best way to go. James -- James Bonfield (j...@sanger.ac.uk) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly
On Wed, Dec 12, 2018 at 11:48:30AM +, James Bonfield wrote: > A simple method is probably the best way to go. +1 Andreas. -- http://fam-tille.de
Processed: Re: Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly
Processing control commands: > tags -1 upstream Bug #916262 [src:staden-io-lib] staden-io-lib: data/xx#unsorted.sam fails randomly Added tag(s) upstream. > forwarded -1 James Bonfield Bug #916262 [src:staden-io-lib] staden-io-lib: data/xx#unsorted.sam fails randomly Set Bug forwarded-to-address to 'James Bonfield '. -- 916262: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=916262 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly
Control: tags -1 upstream Control: forwarded -1 James Bonfield Hi James, besides the remaining build issues on some architectures there is a new bug report about random failures. I hope you will have a clue about this. Kind regards Andreas. On Wed, Dec 12, 2018 at 12:36:43PM +0200, Adrian Bunk wrote: > Source: staden-io-lib > Version: 1.14.11-5 > Severity: serious > Tags: ftbfs > Control: block 912272 by -1 > > https://buildd.debian.org/status/package.php?p=staden-io-lib > https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/staden-io-lib.html > > ... > === testing ./data/xx#unsorted.sam === > ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam > ../progs/scramble test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ../progs/scramble -O bam test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.bam > ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --nopg test.out/xx#unsorted.full.sam > test.out/xx#unsorted.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam > test.out/xx#unsorted.full.bam.sam > > ../progs/scramble -H -r ./data/ce.fa test.out/ce#sorted.full.cram > No region: 1024176 > FAIL: scram.test > ... > === testing ./data/xx#unsorted.sam === > ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam > ../progs/scramble -t4 test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.bam > ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --nopg test.out/xx#unsorted.full.sam > test.out/xx#unsorted.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble -t4 test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam > test.out/xx#unsorted.full.bam.sam > > ../progs/scramble -t4 -H -r ./data/ce.fa test.out/ce#sorted.full.cram > No region: 1024176 > FAIL: scram_mt.test > ... > > > data/xx#unsorted.sam seems to fail randomly, with failures and passes > seen on the same architecture (including amd64). > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly
Source: staden-io-lib Version: 1.14.11-5 Severity: serious Tags: ftbfs Control: block 912272 by -1 https://buildd.debian.org/status/package.php?p=staden-io-lib https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/staden-io-lib.html ... === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -H -r ./data/ce.fa test.out/ce#sorted.full.cram No region: 1024176 FAIL: scram.test ... === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -H -r ./data/ce.fa test.out/ce#sorted.full.cram No region: 1024176 FAIL: scram_mt.test ... data/xx#unsorted.sam seems to fail randomly, with failures and passes seen on the same architecture (including amd64).
