[Debian-med-packaging] [help] Test of samtools breaks build on armel and sparc

[Patrick Baggett]

Looks like SPARC is having a bus error, which almost always means unaligned
data is being accessed. Running this test with gdb attached will break on
the line where there is a problem and should give enough information to the
original developer to resolve it.

Andreas -- can you send me (off-list) steps to reproduce this on my
sparc/sid system?


On Mon, Aug 4, 2014 at 10:30 AM, Andreas Tille <andreas at an3as.eu> wrote:

> Hi,
>
> I realised that the samtools package is not build for armel and sparc[1]
> in both cases since a test running at build time failed:
>
> armel:
>
> make[1]: Entering directory
> `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
> ../samtools faidx ex1.fa
> ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
> [sam_header_read2] 2 sequences loaded.
> Line 2, sequence length 35 vs 8960 from CIGAR
> Parse error at line 2: CIGAR and sequence length are inconsistent
>
>
> sparc:
>
> make[1]: Entering directory
> `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/examples'
> ../samtools faidx ex1.fa
> ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
> [sam_header_read2] 2 sequences loaded.
> make[1]: *** [ex1.bam] Bus error
>
>
> Any hint how to fix this would be welcome.
>
> Kind regards
>
>          Andreas.
>
> [1] https://buildd.debian.org/status/package.php?p=samtools
>
> --
> http://fam-tille.de
>
>
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