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 > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140925131328.gc29...@an3as.eu
