[Debian-med-packaging] Bug#753490: python-pysam FTBFS on mips/mipsel

[Aleksandar Zlicic]

Package: python-pysam
Version: 0.7.7-1
Tags: sid patch
Severity: important
Justification: FTBFS
User: debian-mips-dev-discuss at lists.alioth.debian.org
Usertags: mips-patch
Control: block -1 by 753485

While trying to build python-pysam on mips/mipsel, build fails on testing.

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

The cause of test failures are issues in both 'samtools' and 'python-pysam' packages.

For python-pysam to work samtools has to be fixed first since 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).

python-pysam has unaligned memory access and system endianness related issues as well.
I have attached patches that fix this.

With samtools fixed (with solution proposed at
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753485), and attached patches
are applied to python-pysam, I have successfully built python-pysam on
mips and mipsel.

Could you consider including these patches?

Best regards,
Aleksandar Zlicic
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