[Debian-med-packaging] Bug#797793: samtools update seems to breaks even more tests
Afif Elghraoui
afif at ghraoui.name
Tue Dec 8 05:57:10 UTC 2015
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
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