[Debian-med-packaging] Bug#753485: Bug#753485: samtools: python-pysam FTBFS on mips/mipsel due to issues in samtools

[Aleksandar Zlicic]

Ok, I will contact upstream.

Best Regards
Aleksandar Zlicic
________________________________________
From: Charles Plessy [plessy at debian.org]
Sent: Wednesday, July 02, 2014 3:16 PM
To: Aleksandar Zlicic; 753485 at bugs.debian.org
Subject: Re: [Debian-med-packaging] Bug#753485: samtools: python-pysam FTBFS on mips/mipsel due to issues in samtools

Le Wed, Jul 02, 2014 at 12:30:24PM +0000, Aleksandar Zlicic a écrit :
> Package: samtools
> Version: 0.1.19-1
> Tags: sid patch
> Severity: important
> User: debian-mips-dev-discuss at lists.alioth.debian.org
> Usertags: mips-patch
>
> 'python-pysam' package FTBFS on mips/mipsel due to issues in 'samtools' package.
>
> Build log for 'python-pysam' on mips:
> https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mips&ver=0.7.7-1&stamp=1397894446
> Build log for 'python-pysam' on mipsel:
> https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mipsel&ver=0.7.7-1&stamp=1397887877
>
> Output of samtools executable from samtools package is used as a reference
> during tests in python-pysam (its output is compared with output from
> pysam python module), but samtools has both unaligned memory access
> and system endianness issues.
>
> I have attached patches that fix this. With these patches applied to samtools,
> python-pysam builds fine.

Hi Aleksandar,

I admit that I am a bit worried of applying a patch that I am not able
to review.  Could you ask upstream (https://github.com/samtools/samtools)
to have a look ?

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan