Your message dated Mon, 19 Dec 2016 22:03:48 +0000
with message-id <e1cj628-000f2l...@fasolo.debian.org>
and subject line Bug#848410: fixed in python-biom-format 2.1.5+dfsg-6
has caused the Debian Bug report #848410,
regarding python-biom-format: FTBFS randomly (failing tests)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
848410: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848410
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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looking for now-outdated files...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
--------------------------------------------------------------------------------
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
--- End Message ---
--- Begin Message ---
Source: python-biom-format
Source-Version: 2.1.5+dfsg-6
We believe that the bug you reported is fixed in the latest version of
python-biom-format, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 848...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-biom-format
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 19 Dec 2016 22:29:00 +0100
Source: python-biom-format
Binary: python-biom-format python3-biom-format python-biom-format-doc
biom-format-tools
Architecture: source
Version: 2.1.5+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
biom-format-tools - command-line tools for BIOM format
python-biom-format - Biological Observation Matrix (BIOM) format (Python 2)
python-biom-format-doc - documentation for BIOM format
python3-biom-format - Biological Observation Matrix (BIOM) format (Python 3)
Closes: 848410
Changes:
python-biom-format (2.1.5+dfsg-6) unstable; urgency=medium
.
* Add random seed to test that fails under some circumstances
Closes: #848410
* debhelper 10
* d/watch: version=4
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--- End Message ---
