[Debian-med-packaging] Bug#797793: samtools update seems to breaks even more tests

[Afif Elghraoui]

Hi, Andreas,

على الإثنين  7 كانون الأول 2015 ‫01:10، كتب Andreas Tille:
> 
> Hmmm, I have seen commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8 but I
> remain with failures even on amd64. :-(
> 
> 
> ...
> File "../doc/tss.rst", line 211, in tss.rst
> Failed example:
>     for almnt in sortedbamfile[ window ]:
>         print almnt   #doctest:+ELLIPSIS +NORMALIZE_WHITESPACE
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python2.7/doctest.py", line 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest tss.rst[27]>", line 1, in <module>
>         for almnt in sortedbamfile[ window ]:
>       File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 975, in __getitem__
>         self.sf = pysam.AlignmentFile( self.filename, "rb" )
>     AttributeError: 'module' object has no attribute 'AlignmentFile'
> **********************************************************************


This error appears like you're somehow using an old version of pysam
because AlignmentFile was introduced in 0.8.1. Are you sure you're not
accidentally building with a Jessie chroot (where pysam is at version
0.7.7) rather than an Unstable one?

[...]
> 
> 
> Strange that you can not reproduce this.
> 

I just made sure my working directory was clean and tried building
again. It still works for me...

regards
Afif


-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name