[Debian-med-packaging] Bug#890748: Bug#890748: python-pysam: autopkgtest failures in pbsuite, python-pbcore

[Graham Inggs]

On 18 February 2018 at 19:05, Andreas Tille <andreas at an3as.eu> wrote:
> and see that there are files fitting the libchtslib.*so pattern.
> I have no idea how dynamic linking in this case works - do you
> think some additional symlinks
>
>   ln -s libchtslib.x86_64-linux-gnu.so /usr/lib/python2.7/dist-packages/pysam/libchtslib.so
>   ln -s libchtslib.cpython-36m-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libchtslib.so

I see the following line in python-pysam's build log:

dpkg-shlibdeps: warning: cannot find library libchtslib.so needed by
debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/libcalignedsegment.x86_64-linux-gnu.so
(ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH:
'/usr/lib/python2.7/dist-packages/pysam')

So adding the following line to debian/python-pysam.links might be all
that is needed:
/usr/lib/python2.7/dist-packages/pysam/libchtslib.${DEB_HOST_GNU_TYPE}.so
/usr/lib/python2.7/dist-packages/pysam/libchtslib.so

This should not be needed for Python 3 as it is supposed to be able to
locate modules with the GNU triplet in the name.

I'll test this tomorrow and upload if it works.