[Debian-med-packaging] Bug#848410: python-biom-format: FTBFS randomly (failing tests)
Andreas Tille
andreas at fam-tille.de
Tue Dec 20 07:32:32 UTC 2016
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 <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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