[Debian-med-packaging] Bug#753485: Bug#753485: Status of samtools

[Andreas Tille]

Hi Charles,

On Tue, Sep 16, 2014 at 06:44:23PM +0900, Charles Plessy wrote:
> Le Tue, Sep 16, 2014 at 11:22:50AM +0200, Andreas Tille a écrit :
> > 
> > Yes, seqan is also weiting for MIPS build and I would ping porters about
> > this but according to
> > 
> >    https://buildd.debian.org/status/package.php?p=seqan
> > 
> >   Dependency installability problem for seqan on armel and sparc:
> >   
> >   seqan build-depends on missing:
> >    - libbam-dev
> 
> Hi Andreas,
> 
> since seqan is already not available on armel in jessie, the build failure on
> armel is not blocking.  Se the “excuses” page that only lists mips.
> 
> https://qa.debian.org/excuses.php?package=seqan

I agree with the excuses argument but I wonder what i means that

   https://buildd.debian.org/status/package.php?p=seqan&suite=jessie

shows that seqan was actually built on armel before. 

> Le Tue, Sep 16, 2014 at 11:27:00AM +0200, Andreas Tille a écrit :
> > 
> > On Tue, Sep 16, 2014 at 06:16:54PM +0900, Charles Plessy wrote:
> > > 
> > > Note that libbam-dev is still there, and that seqan seems to be waiting for
> > > mips only.
> > 
> > another issue might be similar:
> > 
> >    https://buildd.debian.org/status/package.php?p=python-biopython
> 
> Here biopython is waiting for samtools (not libbam-dev), probably beause it
> tests a wrapper for it.

Yes, its samtools (I mixed up two different things in one thread,
sorry).  And yes, its testing the wrappers and when I started this we
were able to get rid of *a lot* of bugs in the package.  The only reason
why the current outdated biopython is hanging around in testing is that
nothing is tested. :-(

> Unfortunately, it is not clear to me if samtools
> version 1.0 will build beyond amd64.
> 
> At worse, I can file request for removal on non-amd64 architectures for the
> reverse-depedancies of samtools.

This would be definitely to harsh and actually does not help biopython
at all.  I guess we had a lot of support from upstream regarding patches
for other architectures.  The softest means that would help would simply
to skip the single test for samtools on architectures where we do not
have it.  Please raise your voice about this as soon as you know more
since we really are short in time considering that I'm busy with
biopython for six monthes or more.
 
Kind regards

     Andreas.

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