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-format-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looking for now-outdated files...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-format-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-format-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-format-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/pythonX.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
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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.
python-biom-format_2.1.5+dfsg-5_amd64-20161018T061114Z.gz
Description: application/gzip
python-biom-format_2.1.5+dfsg-5_amd64-20161206T144923Z.gz
Description: application/gzip
python-biom-format_2.1.5+dfsg-5_amd64-20161212T202255Z.gz
Description: application/gzip
python-biom-format_2.1.5+dfsg-5_amd64-20161216T203804Z.gz
Description: application/gzip
