Hi Andreas, I'm cc'ing Daniel McDonald on this message, who is the primary maintainer of the biom-format package these days. Daniel, could you follow up with Andreas?
On Sat, Dec 17, 2016 at 3:53 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Greg, > > the Debian packaged biom-format received a bug report which leaves me > clueless how to track it down. Is there possibly some way to make the > test suite more verbose to find out what part might cause the random > failure which you can see in the buil logs linked from the bug page > > https://bugs.debian.org/848410 > > Thanks for any idea to track this down > > Andreas. > > On Sat, Dec 17, 2016 at 01:34:49PM +0100, Santiago Vila wrote: > > Package: src:python-biom-format > > Version: 2.1.5+dfsg-5 > > Severity: serious > > > > Dear maintainer: > > > > I tried to build this package in stretch with "dpkg-buildpackage -A" > > (which is what the "Arch: all" autobuilder would do to build it) > > but it failed: > > > > ------------------------------------------------------------ > -------------------- > > [...] > > debian/rules build-indep > > dh build-indep --with python2,python3,bash-completion,sphinxdoc > --buildsystem=pybuild > > dh_testdir -i -O--buildsystem=pybuild > > dh_update_autotools_config -i -O--buildsystem=pybuild > > dh_auto_configure -i -O--buildsystem=pybuild > > pybuild --configure --test-nose -i python{version} -p 2.7 > > I: pybuild base:184: python2.7 setup.py config > > running config > > pybuild --configure --test-nose -i python{version} -p 3.5 > > I: pybuild base:184: python3.5 setup.py config > > running config > > debian/rules override_dh_auto_build > > make[1]: Entering directory '/<<BUILDDIR>>/python-biom- > format-2.1.5+dfsg' > > > > [... snipped ...] > > > > ImportError: No module named _filter > > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/doc/ > documentation/table_objects.rst:1: WARNING: autodoc: failed to import > module u'biom.table'; the following exception was raised: > > Traceback (most recent call last): > > File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line > 526, in import_object > > __import__(self.modname) > > File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/biom/__init__.py", > line 53, in <module> > > from .table import Table > > File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/biom/table.py", > line 195, in <module> > > from ._filter import _filter > > ImportError: No module named _filter > > looking for now-outdated files... none found > > pickling environment... done > > checking consistency... done > > writing... biom.1 { documentation/index documentation/biom_format > documentation/format_versions/biom-1.0 documentation/format_versions/biom-2.0 > documentation/format_versions/biom-2.1 documentation/quick_usage_examples > documentation/table_objects documentation/biom_conversion > documentation/adding_metadata documentation/summarizing_biom_tables > BIOM_LICENSE } > > build succeeded, 3 warnings. > > make[1]: Leaving directory '/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg' > > dh_auto_test -i -O--buildsystem=pybuild > > pybuild --test --test-nose -i python{version} -p 2.7 > > I: pybuild pybuild:212: cp -r > > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/examples > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/tests > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build > > I: pybuild base:184: cd /<<BUILDDIR>>/python-biom- > format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests > > ............................................................ > ............................................................ > ............................................................ > ............................................................ > ...........S............. > > ---------------------------------------------------------------------- > > Ran 265 tests in 3.736s > > > > OK (SKIP=1) > > pybuild --test --test-nose -i python{version} -p 3.5 > > I: pybuild pybuild:212: cp -r > > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/examples > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/tests > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build > > I: pybuild base:184: cd /<<BUILDDIR>>/python-biom- > format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose tests > > ............................................................ > ............................................................ > ............................................................ > ............................................................ > ...........S......F...... > > ====================================================================== > > FAIL: test_generate_subsamples (tests.test_util.UtilTests) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/ > pythonX.Y_3.5/build/tests/test_util.py", line 58, in > test_generate_subsamples > > (3, 1, 1)}) > > AssertionError: Items in the second set but not the first: > > (3, 0, 0) > > > > ---------------------------------------------------------------------- > > Ran 265 tests in 3.575s > > > > FAILED (SKIP=1, failures=1) > > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: > cd /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build; > python3.5 -m nose tests > > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 > returned exit code 13 > > debian/rules:18: recipe for target 'build-indep' failed > > make: *** [build-indep] Error 25 > > dpkg-buildpackage: error: debian/rules build-indep gave error exit > status 2 > > ------------------------------------------------------------ > -------------------- > > > > The failure happens randomly on the single-CPU KVM/QEMU virtual machines > > I use as autobuilders. The approximate failure rate is about 1%. > > > > I attach several build logs (made on different autobuilders). > > > > If you could not reproduce this using sbuild on a single CPU virtual > > machine (as I did), of course trying a lot of times (because of the > > failure rate above), please do not downgrade or mark as unreproducible, > > I would then consider giving you access to a virtual machine on which > > I can reproduce it so that you can as well. (In such case, please > > contact me off-list for details). > > > > Thanks. > > > > > > > _______________________________________________ > > 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 >
