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

[Afif Elghraoui]

Hi, Andreas,

على الأحد  6 كانون الأول 2015 ‫13:11، كتب Andreas Tille:
>>> Any idea how to fix this.  Htslib upstream is unresponsive even to less
>>> hard issues.
>>>

I was confused that you were referring to this package as Htslib (I
think you also did so in your message to upstream)-- you mean Htseq
here. I don't know if others were similarly confused.

>>
>> The recent pysam release dropped support for some deprecated interfaces
>> and this package appears to have been affected. I can prepare a patch
>> for those pysam issues as I did for pbcore [1]
> 
> A patch would be cool - this would help in the advent bug squashing
> effort. :-)

I sent an email around the same time as yours announcing the patch is in
git. I didn't realize this was the central issue of the bug report. If
that's the case, I think you should just add the "Closes..." statement
to the changelog. :)


>  
>> By the way, I had checked rdepends of pysam to look out for packages
>> that may have problems later on due to the change, but the only way I
>> know how to do that is using apt-cache rdepends. This has limitations
>> because I use Stable and can't get an up-to-date report without changing
>> my sources.list
> 
> You could create an unstable chroot and login via dchroot.  At least
> that's my way to have an unstable system at hand.
>

Thanks for the tip.

regards
Afif

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