Re: Help to run test suite for python-pysam needed (does not find libhts) (Was: 01/01: Reenable check to ask for help on Debian Python list)
Le Sat, Sep 27, 2014 at 07:35:23PM +0200, Andreas Tille a écrit :
>
> > Then, trying to build the binary package I reproduced the problem of missing
> > the faidx_fetch_nseq symbol. When uploading libhts1 version 1.1 I actually
> > noticed that the symbol was dropped (thanks to the libhts1.symbols file), but
> > hoped that the reason why the upstream authors did not bump the soname of their
> > library after that backwards-incompatible change was that they knew it was not
> > problematic. As it turns out, pysam needed it… This said, given that the the
> > HTSlib 1.0 was only out for a few weeks, I think that the best is to move
> > forward by updating pysam to the HTSlib 1.1. This is done easily with
> > s/faidx_fetch_nseq/faidx_nseq/.
> >
> > Then, the package builds but some tests fail after trying to access a remote
> > file.
>
> OK, we need to skip thoise tests (or even better ask upstream for an
> option to exclude tests needing online connection).
Hi Andreas,
skipping online tests would be straightforward with patches such as the one I
just proposed upstream.
https://github.com/pysam-developers/pysam/issues/42
However, the latest Pysam fails a lot of other tests by producing an output
that it not exactly the same as in Samtools 1.1. I do not know if this will be
solved upstream on time for our freeze…
> I'd really like to get this out as fast as possible. I have some
> packages depending from python-pysam which I really want to let migrate
> as soon as possible.
Do you mean that they need pysam 0.8 ? Because otherwise I do not see how
pysam is blocking them: currently version 0.7.7-1 is in both Testing and Sid.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Reply to: