Bug#713085: pytables: FTBFS: tests failed
Antonio Valentino
antonio.valentino at tiscali.it
Sat Jun 22 16:39:35 UTC 2013
Hi,
Il 22/06/2013 13:11, Lucas Nussbaum ha scritto:
> Source: pytables
> Version: 2.3.1-3
> Severity: serious
> Tags: jessie sid
> User: debian-qa at lists.debian.org
> Usertags: qa-ftbfs-20130620 qa-ftbfs
> Justification: FTBFS on amd64
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
>
> Relevant part:
>> make[1]: Entering directory `/«PKGBUILDDIR»'
>> # Install everything excluding the *_d.so debug extensions to python-tables
>> dh_install -X"*_d.so" "debian/tmp/*" -p python-tables
>> # Install the debug extensions to python-tables-dbg
>> dh_install "debian/tmp/usr/lib/python*/*-packages/tables/*_d.so" -p python-tables-dbg
>> # Continue with regular dh_install
>> dh_install -p python-tables-doc
>> dh_numpy
>> set -e -x; \
>> for py in 2.7; do \
>> cd "/«PKGBUILDDIR»/debian/tmp/usr/lib/python$py/dist-packages/"; \
>> env PYTHONPATH=. python$py tables/tests/test_all.py -vvv; \
>> #env PYTHONPATH=. python$py-dbg tables/tests/test_all.py; \
>> done
>> + cd /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/
>> + env PYTHONPATH=. python2.7 tables/tests/test_all.py -vvv
[CUT]
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>> PyTables version: 2.3.1
>> HDF5 version: 1.8.10-patch1
>> NumPy version: 1.7.1
>> Numexpr version: 2.0.1 (not using Intel's VML/MKL)
>> Zlib version: 1.2.8 (in Python interpreter)
>> LZO version: 2.06 (Aug 12 2011)
>> BZIP2 version: 1.0.6 (6-Sept-2010)
>> Blosc version: 1.1.2 (2010-11-04)
>> Cython version: 0.19
>> Python version: 2.7.5+ (default, Jun 13 2013, 13:26:49)
>> [GCC 4.8.1]
>> Platform: linux2-x86_64
>> Byte-ordering: little
>> Detected cores: 1
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>> Performing only a light (yet comprehensive) subset of the test suite.
>> If you want a more complete test, try passing the --heavy flag to this script
>> (or set the 'heavy' parameter in case you are using tables.test() call).
>> The whole suite will take more than 4 hours to complete on a relatively
>> modern CPU and around 512 MB of main memory.
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
[CUT]
>> ======================================================================
>> ERROR: None (tables.tests.test_array.FancySelection1)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 250, in newmethod
>> return oldmethod(self, *args, **kwargs)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/test_array.py", line 2191, in test01d_read
>> self.assertRaises(ValueError, nparr.__getitem__, key)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 398, in failUnlessRaises
>> excClass, callableObj, *args, **kwargs)
>> File "/usr/lib/python2.7/unittest/case.py", line 475, in assertRaises
>> callableObj(*args, **kwargs)
>> IndexError: too many indices for array
>>
>> ======================================================================
>> ERROR: None (tables.tests.test_array.FancySelection2)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 250, in newmethod
>> return oldmethod(self, *args, **kwargs)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/test_array.py", line 2191, in test01d_read
>> self.assertRaises(ValueError, nparr.__getitem__, key)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 398, in failUnlessRaises
>> excClass, callableObj, *args, **kwargs)
>> File "/usr/lib/python2.7/unittest/case.py", line 475, in assertRaises
>> callableObj(*args, **kwargs)
>> IndexError: too many indices for array
>>
>> ======================================================================
>> ERROR: None (tables.tests.test_array.FancySelection3)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 250, in newmethod
>> return oldmethod(self, *args, **kwargs)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/test_array.py", line 2191, in test01d_read
>> self.assertRaises(ValueError, nparr.__getitem__, key)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 398, in failUnlessRaises
>> excClass, callableObj, *args, **kwargs)
>> File "/usr/lib/python2.7/unittest/case.py", line 475, in assertRaises
>> callableObj(*args, **kwargs)
>> IndexError: too many indices for array
>>
>> ======================================================================
>> ERROR: None (tables.tests.test_array.FancySelection4)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 250, in newmethod
>> return oldmethod(self, *args, **kwargs)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/test_array.py", line 2191, in test01d_read
>> self.assertRaises(ValueError, nparr.__getitem__, key)
>> File "/«PKGBUILDDIR»/debian/tmp/usr/lib/python2.7/dist-packages/tables/tests/common.py", line 398, in failUnlessRaises
>> excClass, callableObj, *args, **kwargs)
>> File "/usr/lib/python2.7/unittest/case.py", line 475, in assertRaises
>> callableObj(*args, **kwargs)
>> IndexError: too many indices for array
>>
>> ----------------------------------------------------------------------
>> Ran 4728 tests in 214.922s
>>
>> FAILED (errors=4)
>> make[1]: *** [override_dh_install] Error 1
>
> The full build log is available from:
> http://aws-logs.debian.net/ftbfs-logs/2013/06/20/pytables_2.3.1-3_unstable.log
>
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
>
OK, the issue is related to a small incompatibility with numpy > 1.6.1
(see [1]) and it has been fixed upstream in PyTables 3.0.
We are currently working on the package for PyTables 3.0 but it
introduces some API changes so it can't be uploaded to sid right now.
The problem is only in the test code and it can be fixed with a one-line
patch [2].
I can prepare a patched package for PyTables 2.3.1, but it is probably a
good idea to upload a package for PyTables 2.4 that is in experimental
since long time (it still needs to be patched for the specific issue).
What do you think about it?
best regards
[1] https://github.com/PyTables/PyTables/issues/162
[2]
https://github.com/PyTables/PyTables/commit/44de7c1ef6dca455cd6c7cf090f9411929d8a115
--
Antonio Valentino
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