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

[Andreas Tille]

Hi,

in Git[1] I tried to implement the additional hint from upstream

   https://github.com/pysam-developers/pysam/issues/34

but this does not change anything. :-(

Any further help would be welcome

        Andreas.

On Thu, Sep 25, 2014 at 02:48:25PM +0200, Andreas Tille wrote:
> Hi,
> 
> I tried to upgrade python-pysam[1] but the build endet in a failed test
> suite:
> 
> 
> LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
> 	--test-args='set -e; \
> 		     cp -a /tmp/buildd/python-pysam-0.8.0/tests {build_dir}/tests ; \
> 		     cd {build_dir}/tests && PYTHONPATH={build_dir} {interpreter} ./pysam_test.py \
> 		                          && PYTHONPATH={build_dir} {interpreter} ./tabix_test.py '
> I: pybuild base:170: set -e; \
> 		     cp -a /tmp/buildd/python-pysam-0.8.0/tests /tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/tests ; \
> 		     cd /tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/tests && PYTHONPATH=/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build python2.7 ./pysam_test.py \
> 		                          && PYTHONPATH=/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build python2.7 ./tabix_test.py.
> Traceback (most recent call last):
>   File "./pysam_test.py", line 8, in <module>
>     import pysam
>   File "/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py", line 5, in <module>
>     import pysam.csamfile as csamfile
>   File "cfaidx.pxd", line 14, in init pysam.csamfile (pysam/csamfile.c:39867)
> ImportError: /tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so: undefined symbol: faidx_fetch_nseq
> E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: set -e; \
> 		     cp -a /tmp/buildd/python-pysam-0.8.0/tests /tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/tests ; \
> 		     cd /tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build/tests && PYTHONPATH=/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build python2.7 ./pysam_test.py \
> 		                          && PYTHONPATH=/tmp/buildd/python-pysam-0.8.0/.pybuild/pythonX.Y_2.7/build python2.7 ./tabix_test.py.
> dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=set -e; \
> 		     cp -a /tmp/buildd/python-pysam-0.8.0/tests {build_dir}/tests ; \
> 		     cd {build_dir}/tests && PYTHONPATH={build_dir} {interpreter} ./pysam_test.py \
> 		                          && PYTHONPATH={build_dir} {interpreter} ./tabix_test.py  --dir . returned exit code 13
> debian/rules:32: recipe for target 'override_dh_auto_test' failed
> make[1]: *** [override_dh_auto_test] Error 13
> make[1]: Leaving directory '/tmp/buildd/python-pysam-0.8.0'
> debian/rules:11: recipe for target 'build' failed
> make: *** [build] Error 2
> 
> 
> 
> The problem seems to be that the library libhts is not properly linked
> since
> 
> $ strings /usr/lib/x86_64-linux-gnu/libhts.so.1 | grep faidx_fetch_nseq
> faidx_fetch_nseq
> 
> 
> Any idea why this library is not found?
> 
> Kind regards
> 
>         Andreas.
> 
> 
> [1] git://git.debian.org/git/debian-med/python-pysam.git
> 
> -- 
> http://fam-tille.de
> 
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