[Debian-med-packaging] Bug#912451: staden-io-lib FTBFS on !x86: test failures

[Andreas Tille]

Hi James,

On Mon, Nov 26, 2018 at 09:39:33AM +0000, James Bonfield wrote:
> I looked at this and don't see test failures, only "build attempted".
> Has it changed since this email?

The "Build-Attempted" fields are links for instance to

   https://buildd.debian.org/status/fetch.php?pkg=staden-io-lib&arch=arm64&ver=1.14.11-1&stamp=1540934378&raw=0

Just scroll to nearly end or seek for the strings mentioned below.

Kind regards

       Andreas.
 
> > and this is basically the failure.  Do you have any idea how to fix this?
> > 
> > ...
> > FAIL: scram
> > ===========
> > 
> > Loading ce.fa
> > Generating ce#sorted.sam
> > Generating ce#unsorted.sam
> > === testing ./data/c1#bounds.sam ===
> > ./scram.test: 27: [: ./data/c1#bounds.sam: unexpected operator
> >  ../progs/scramble  ./data/c1#bounds.sam test.out/c1#bounds.sam
> >  ../progs/scramble  -r ./data/c1.fa ./data/c1#bounds.sam test.out/c1#bounds.full.cram
> >  ../progs/scramble  ./data/c1#bounds.sam > test.out/tmp.sam
> >  ../progs/scramble  test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> >  ../progs/scramble  -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
> >  ../progs/scramble  test.out/c1#bounds.full.bam test.out/tmp.sam
> > corrupted size vs. prev_size
> > Aborted
> > FAIL scram.test (exit status: 1)
> 
> I'm also struggling to find the "corrupted size vs. prev_size" error
> message anywhere in the code, not even "prev_size".
> 
> Googling for it I finally found it listed as an error in GNU malloc,
> which possibly means there is a memory corruption. I will run through
> the entire test harness using address sanitiser and if that doesn't
> work with Valgrind.
> 
> 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 
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> 

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