[Debian-med-packaging] Bug#813262: python-biopython: FTBFS: ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa'

[Peter Cock]

On Mon, Feb 1, 2016 at 12:08 PM, Andreas Tille <andreas at an3as.eu> wrote:
> Hi Peter,
>
> ...
>
> Yes.  BioPython is OK - I need to reassign the bug - probably to
> libhmsbeagle-dev which is possibly not featuring the correct
> dependencies.  I just wanted to investigate the issue before I
> do the reassigning since for the moment it is just the BioPython
> *package* *in* *debian* that fails.

Understood.

> ...
>
> My plan for this years GSoC is to find a student who could add as much
> testing to Debian Med packages as possible.  In this sense BioPython is
> a great test suite since it somehow adds tests to those packages that
> come without one. :-)

Nice idea. We might be able to do that under the Open Bioinformatics
Foundation as a GSoC umbrella organisation if we're accepted into
GSoC this year [I'm not directly involved but am on the OBF board]:

http://mailman.open-bio.org/pipermail/open-bio-l/2016-January/001423.html

The Biopython tests here are generally for our command line tool
wrappers (and often catch changes to their command line API),
and/or checking we can parse the latest output from the command
line tools (Bioinformatics file formats are sadly often fluid).

> Thanks again for getting involved into this bug report.  I think
> I will use the upcoming Debian Med sprint[1] to sort these things
> out.

I hope to come along to another Debian Med sprint next time
one's close to home :)

Thanks,

Peter