[Debian-med-packaging] Help to run test suite for python-pysam needed (does not find libhts)

[Gert Wollny]

Hi Andreas, 

I can confirm that this problem doesn't show up in an up-to-date sid. 
Cython has a new version there as compared to todays testing, but
installing this new version in testing didn't resolve the problem. 

Anyway, the other question was about the missing symbol faidx_fetch_nseq
in htslib-1.1. 

Well, the function is declared in one of the htslibs headers, but no
function body is defined in the whole of the library source code, i.e.
within its source tree I get: 

grep -r faidx_fetch_nseq  *
debian/libhts1.symbols:#MISSING: 1.1# faidx_fetch_nseq at Base 1.0
htslib/faidx.h:    int faidx_fetch_nseq(const faidx_t *fai);

According to this commit in the htslib repo [1] the function name has
been replaced by "faidx_nseq" but it was not deleted from the header. 

Hope that helps,
Gert 



[1]
https://github.com/samtools/htslib/commit/5a0ee032c4e94f5b2814c6f389278b404f439713



On Thu, 2014-09-25 at 19:43 +0200, Andreas Tille wrote:
> Hi Gert,
> 
> On Thu, Sep 25, 2014 at 06:13:19PM +0200, Gert Wollny wrote:
> > I got this: 
> > 
> > Traceback (most recent call last):
> >   File "tests/pysam_test.py", line 15, in <module>
> >     from TestUtils import checkBinaryEqual
> > ImportError: No module named TestUtils
> > 
> > and I saw that you had this too before [1], but the answer was missing. 
> > How did you solve this? Would the solution need a package from sid?
> 
> I confirm that this problem existed but is now present any more in an up
> to date sid chroot.  I do not remember that I have done any means to
> work around this.
> 
> Kind regards
> 
>        Andreas.
>  
> > [1]http://web.archiveorange.com/archive/v/WK9riEUrSSGTqb90VM4v
> > 
> > 
> > On Thu, 2014-09-25 at 16:22 +0200, Andreas Tille wrote:
> > > Ups, sorry, done.  Andreas.
> > > 
> > > On Thu, Sep 25, 2014 at 03:32:49PM +0200, Gert Wollny wrote:
> > > > Hi Andreas, 
> > > > 
> > > > 
> > > > I tried to have a look, but ... 
> > > > 
> > > > 
> > > > On Thu, 2014-09-25 at 14:48 +0200, Andreas Tille wrote:
> > > > > [1] git://git.debian.org/git/debian-med/python-pysam.git
> > > > > 
> > > > Could you "git push --all --tags", because git doesn't have the
> > > > upstream/0.8.0 version tagged. 
> > > > 
> > > > best 
> > > > Gert 
> > > > 
> > > > 
> > > 
> > > 
> > > 
> > 
> 
> 
> 

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