Re: Python-pysam for unstable?

[Andreas Tille <andreas@an3as.eu>]

Hi Afif,

On Sun, Jul 12, 2015 at 12:39:22PM -0700, Afif Elghraoui wrote:
> Hi, Andreas,
> 
> I have created a branch where I've restored the python-pysam-tests package.
> The tests there still do not run, but it is mostly the way it was before. I
> have added to debian/rules to build the test data, which is necessary for
> that configuration.

Thanks, I'll check out this tomorrow.
 
> In the master branch (no additional test package), there is some test that
> fails on a gcc call. Other tests fail due to python keyerrors, and it will
> take some debugging that I don't have a chance for right now.

I did some small test and got some:

/usr/lib/python2.7/dist-packages/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/TabProxies.so: Datei oder Verzeichnis nicht gefunden
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/cfaidx.so: Datei oder Verzeichnis nicht gefunden
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/csamfile.so: Datei oder Verzeichnis nicht gefunden
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/cvcf.so: Datei oder Verzeichnis nicht gefunden
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/cbcf.so: Datei oder Verzeichnis nicht gefunden
x86_64-linux-gnu-gcc: error: /usr/lib/python2.7/dist-packages/pysam/ctabix.so: Datei oder Verzeichnis nicht gefunden

(the message means "File or directory not found")

This is pretty strange and I was able to cure this by


cd /usr/lib/python2.7/dist-packages/pysam
gnutype=`dpkg-architecture -qDEB_TARGET_GNU_TYPE`
for so in *.${gnutype}.so ; do sudo ln -sf $so `basename $so .${gnutype}.so`.so ; done


I wonder if this is really some problem.  Need to investigate this
tomorrow - just wanted to tell that I did some bit without real news.
 
> >Could you publish a log of the failed tests?
> 
> Please see attached.

Thanks, will look into this tomorrow.

Kind regards

       Andreas.


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