[Debian-med-packaging] Bug#916262: staden-io-lib: data/xx#unsorted.sam fails randomly

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 James Bonfield <jkb at sanger.ac.uk>

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).
> 
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