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 -- 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/20140925124825.ga29...@an3as.eu