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

[James Bonfield]

Hello Andreas,

On Mon, Nov 26, 2018 at 08:08:44AM +0100, Andreas Tille wrote:
> version 1.14.11 of staden-io-lib creates an error in the test suite for non x86
> architectures.  Here you have an easy overview what architectures are affected:
> 
>    https://urldefense.proofpoint.com/v2/url?u=https-3A__buildd.debian.org_status_package.php-3Fp-3Dstaden-2Dio-2Dlib-26suite-3Dsid&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=L-jZYyQAt7E4nbUsttBpOY_Mp4v3CCgPpbF36FyJveI&s=-atiCd8AX9Plf89RpXOx6vaJ9hAbqKhJ27ntOhiECy4&e=

Sorry for the butchered URL.  I hate our new email scanning!
I looked at this and don't see test failures, only "build attempted".
Has it changed since this email?

> 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


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