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

[Andreas Tille]

Hi Afif,

On Sun, Dec 06, 2015 at 11:35:09AM -0800, Afif Elghraoui wrote:
> >     NameError: name 'start_in_window' is not defined
> 
> [...]
> > 
> > Any idea how to fix this.  Htslib upstream is unresponsive even to less
> > hard issues.
> > 
> 
> 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. :-)
 
> 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.

Kind regards

       Andreas.
 

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