[Debian-med-packaging] Bug#848410: python-biom-format: FTBFS randomly (failing tests)

Mon Dec 19 18:25:10 UTC 2016

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 <gregcaporaso at 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 <andreas at 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-packaging at lists.alioth.debian.org
>> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debi
>> an-med-packaging
>>
>>
>> --
>> http://fam-tille.de
>>
>
>
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