Thanks, Greg. Andreas, the particular test that is failing as it is stochastic. It is likely possible to just set a random seed at entry into the test here:
https://github.com/biocore/biom-format/blob/master/tests/test_util.py#L48 Specifically, doing something like "np.random.seed(123)" Best, Daniel On Tue, Dec 20, 2016 at 5:15 AM, Greg Caporaso <gregcapor...@gmail.com> wrote: > 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-for >> mat-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-for >> mat-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-form >> at-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-form >> at-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/python >> X.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/debi >> an-med-packaging >> >> >> -- >> http://fam-tille.de >> > >
