[Debian-med-packaging] [wrar at debian.org: Re: Dynamic library inside Python module python-pysam not found]

[Afif Elghraoui]

Hi, Andreas,I believe HTSLIB_MODE=external is already set in debian/rules.As for the htslib 1.3.2 support, see the release notes for this version at http://github.com/pysam-developers/pysam/releases
I've worked around this multi-arch renaming issue a couple times before. For example, muliarch-module-path.patch in pbh5tools.
I will see when I get a chance.
Afif

Sent from my T-Mobile 4G LTE Device-------- Original message --------From: Andreas Tille <andreas at an3as.eu> Date: 1/25/2017  13:14  (GMT-08:00) To: Afif Elghraoui <afif at debian.org>, Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org> Subject: [wrar at debian.org: Re: [Debian-med-packaging] Dynamic library inside
  Python module python-pysam not found] 
Hi Afif,

may be this mail contains some helpful hint since it seems that the lib
libchtslib.so simly should not be created at all.  I tried my luck with
setting 

   HTSLIB_MODE = "external"

but this did not lead to any sensible result.

Please also note that setup.py says

   The current version wraps htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1.
                                    ^^^^^

so I have no idea where you've git the information from that 1.3.2 is
supported.

I'll leave this now for others who might have a better clue than me.

Kind regards

       Andreas.

----- Forwarded message from Andrey Rahmatullin <wrar at debian.org> -----

Date: Wed, 25 Jan 2017 22:00:51 +0500
From: Andrey Rahmatullin <wrar at debian.org>
To: debian-mentors at lists.debian.org
Subject: Re: [Debian-med-packaging] Dynamic library inside Python module python-pysam not found

On Wed, Jan 25, 2017 at 05:28:34PM +0100, Andreas Tille wrote:
> > > tests of python-pbcore failed with
> > >
> > >   ERROR: Failure: ImportError (libchtslib.so: cannot open shared object file: No such file or directory)
> > >
> > > When installing python-pysam 0.10.0+ds-1 I get
> > >
> > > $ ls -l /usr/lib/python2.7/dist-packages/pysam/libchtslib.*.so
> > > -rw-r--r-- 1 root root 103864 Jan 24 04:13 /usr/lib/python2.7/dist-packages/pysam/libchtslib.x86_64-linux-gnu.so
> > Certainly because at build time it compiles against libchtslib.so
> > provided by a -dev package and keeps this reference instead of using
> > "real" library file libchtslib.x86_64-linux-gnu.so
> 
> I can confirm that there is a hack around this by simply doing
> 
>    ln -s libchtslib.x86_64-linux-gnu.so /usr/lib/python2.7/dist-packages/pysam/libchtslib.so
> 
> but what would be the "clean" solution for this problem?
First you need to find out if that lib is some useful code or a copy of
libhts that for some reason got built and used even with
HTSLIB_MODE=external.
If it should still be built, then it's either a shared lib and then it
doesn't belong in dist-packages, or a python module and then it shouldn't
ne linked against.

-- 
WBR, wRAR



----- End forwarded message -----

-- 
http://fam-tille.de
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