Your message dated Mon, 19 Dec 2016 22:03:48 +0000 with message-id <[email protected]> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 848410: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848410 Debian Bug Tracking System Contact [email protected] 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 from ._filter import _filter ImportError: No module named _filter looking for now-outdated files...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
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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 Checksums-Sha1: 54c45e32b70b65be009a7f337eb53ee2c3125b00 2999 python-biom-format_2.1.5+dfsg-6.dsc 8985d7c96b92065211902e6dc7711443a46d17b3 8156 python-biom-format_2.1.5+dfsg-6.debian.tar.xz Checksums-Sha256: 62a152149f09afba4b772273184ebf94b91f919ab68e880a3673f594368d3b93 2999 python-biom-format_2.1.5+dfsg-6.dsc ae65f7b05fa471fec4b81372c1f876a53e6ec4eb44ad4c30365925db807de691 8156 python-biom-format_2.1.5+dfsg-6.debian.tar.xz Files: 8e74f53681b9082c12a39ef40051009f 2999 python optional python-biom-format_2.1.5+dfsg-6.dsc 6a743162f19c1e017705eaec8968c168 8156 python optional python-biom-format_2.1.5+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlhYU7QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFGjQ//WRe54ndAL+1pGhg1ysIIN2kZcAPss4Ig vkYIjPWHNq+ZGk6S3M+Qy4pt5Bx0CE6mhKCrd+0jOSXAj5cnPXji6D8jfjmnrH2K p81DYsBrz1jDssCA10w4kem6kuIUNXo4IYzD3/dRWY/utQBACqzRT/HqBVDMssCu cxmqaFsbwzBENgMFL03nj8tVzjLo/zIbgxWA6IvDik9HAY+CkYdUqJYX3q8z4Nkw JuSwudgT809UEPHMSVMQKePYyxCQqfTGNn5YP0tG9acDzw2HjJpXKp4Pi5tL1oBe RxFOR98s/f9MZByYKCvGgn5Xmh3MggOPI+GpTdLys8eqMeI9Tlh4BbvcEPsUWIk7 PeqYuYS0FBE7A6IKGwcAMxoB3Igj5p3341V8eBJc6JZpYJqnx1UqJvbc5sQPgtE0 fYEk046Vnu7zn4WssRNjQ3qfJ12ciEjRrLBl8l8v+LXB62mrRn2FkfqvywD+Mofk EQS0za9HPt7w1BOB5J8e02ALCeI1DJ4YlJeDMfxMWo2ztMSRpgyQrfO+GAORVveZ nUIXGS5Ymnqp6lcFDJ95eb5RSKd2+muOfc2IW02n/yucNmfBV3xgcw2qqebfWxGc ZTRsoFcgo/DHekhh8qMsyPawoshS8iLN+gkgLbOXP+TgdYrD6jivAeMTT4fC01Kc KrXYkY0oH3A= =gPGc -----END PGP SIGNATURE-----
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