Hi Daniel, thanks for the helpful hint. I've uploaded a package with the suggested fix and I hope this random error will be solved now. However, there seems to be another issue which happens on i386 architecture only:
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 2.759s 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 ..................................................................................................................................................F........................................................................................................S............. ====================================================================== FAIL: test_subsample (tests.test_table.SparseTableTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_table.py", line 2263, in test_subsample (3, 1, 1)}) AssertionError: Items in the second set but not the first: (3, 0, 0) ---------------------------------------------------------------------- Ran 265 tests in 3.098s FAILED (SKIP=1, failures=1) You can find the full build log here: https://buildd.debian.org/status/fetch.php?pkg=python-biom-format&arch=i386&ver=2.1.5%2Bdfsg-6&stamp=1482186822 Any idea what might be wrong here? Kind regards Andreas. On Tue, Dec 20, 2016 at 05:25:10AM +1100, Daniel McDonald wrote: > 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 > >> > > > > -- http://fam-tille.de