Hi Daniel, thanks for the quick response.
On Mon, Dec 19, 2016 at 11:42:33PM -0800, Daniel McDonald wrote: > Try a different seed? Same issue: it's a stochastic test. Hmmm, shouldn't the verification routine of the test result be able to cope with the randomness instead to fail for a random set of seeds? I simply sticked to your 123 example for the seed in the patch I uploaded: https://anonscm.debian.org/cgit/debian-med/python-biom-format.git/tree/debian/patches/random_seed_for_test.patch I'm now wondering what might be a more promissing guess for the seed and moreover the failure was in a different test file than I have patched - so may be several tests would need a seed, right? > Other option is > bump the number of iterations it performs. Could you provide a patch that implements this. Kind regards Andreas. > Best, > Daniel > > On Dec 19, 2016 23:32, "Andreas Tille" <andr...@fam-tille.de> wrote: > > > 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 > > > _______________________________________________ > 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