[Debian-med-packaging] Dynamic library inside Python module python-pysam not found

[Olivier Sallou]

On 01/25/2017 04:17 PM, Andreas Tille wrote:
> Hi,
>
> I'm trying to upgrade the python-pysam package.  When I build the
> current status in Git[1] the package builds fine.  However I tried to
> build python-pbcore that Build-Depends python-pysam and the build time
> 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

Olivier
> $ ldd /usr/lib/python2.7/dist-packages/pysam/*.so | grep -e ^/ -e "not found"
> /usr/lib/python2.7/dist-packages/pysam/libcalignedsegment.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcalignmentfile.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcbcf.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcbgzf.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcfaidx.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libchtslib.x86_64-linux-gnu.so:
> /usr/lib/python2.7/dist-packages/pysam/libcsamfile.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libctabixproxies.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libctabix.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcutils.x86_64-linux-gnu.so:
>         libchtslib.so => not found
> /usr/lib/python2.7/dist-packages/pysam/libcvcf.x86_64-linux-gnu.so:
>         libchtslib.so => not found
>
>
> I'm wondering why libchtslib is not found by all those dynamic libs.
>
> Any help is welcome
>
>         Andreas.
>
>
> [1] https://anonscm.debian.org/git/debian-med/python-pysam.git
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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