[Debian-med-packaging] Bug#915459: staden-io-lib FTBFS on armhf/sparc64: Bus error

[James Bonfield]

On Tue, Dec 04, 2018 at 07:54:25AM +0100, Andreas Tille wrote:
> > === testing ./data/c1#bounds.sam ===
> > ./scram.test: 27: [: ./data/c1#bounds.sam: unexpected operator
> >  ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.sam
> >  ../progs/scramble -t4 -r ./data/c1.fa ./data/c1#bounds.sam test.out/c1#bounds.full.cram
> >  ../progs/scramble -t4 ./data/c1#bounds.sam > test.out/tmp.sam
> >  ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> > Bus error
> > FAIL scram_mt.test (exit status: 1)

Bug identified and fixed in upstream commit 37b33d3.
Thanks for the bug report.

It turned out to not be a multi-threading issue per-se, but rather my
use of a pooled memory allocator when working in a threaded
environment.  I forgot to ensure all my pooled structures were word
aligned.

James

-- 
James Bonfield (jkb at 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.