[Debian-med-packaging] Problems in python-biom-format tests for several architectures

[Andreas Tille]

Hi Tim,

currently qiime is in danger to be removed from testing since
python-biom-format does not migrate to testing due to some test failures
on several architectures (i386, armel, armhf, mips, mipsel, powerpc,
ppc64).  Most 64 bit architectures (but not all - see ppc64) are
passing.  In i386 the test failures are looking like:


dh_auto_test
I: pybuild base:184: cd /«BUILDDIR»/python-biom-format-2.1.4+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests
....................F........F.F..............................................................................................................................................................................................................S.............
======================================================================
FAIL: Test an invalid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/«BUILDDIR»/python-biom-format-2.1.4+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_commands/test_table_validator.py", line 95, in test_invalid_hdf5
    self.assertEqual(obs, exp)
AssertionError: {'valid_table': False, 'report_lines': ["'shape' values do not appear to be inte [truncated]... != {'valid_table': False, 'report_lines': ["Missing attribute: 'creation-date'"]}
+ {'report_lines': ["Missing attribute: 'creation-date'"], 'valid_table': False}
- {'report_lines': ["'shape' values do not appear to be integers",
-                   'nnz is not an integer!',
-                   "Missing attribute: 'creation-date'"],
-  'valid_table': False}

======================================================================
FAIL: Test a valid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/«BUILDDIR»/python-biom-format-2.1.4+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_commands/test_table_validator.py", line 79, in test_valid_hdf5
    self.assertEqual(obs, exp)
AssertionError: {'valid_table': False, 'report_lines': ["'shape' values do not appear to be inte [truncated]... != {'valid_table': True, 'report_lines': []}
+ {'report_lines': [], 'valid_table': True}
- {'report_lines': ["'shape' values do not appear to be integers",
-                   'nnz is not an integer!'],
-  'valid_table': False}

...



The problem is now:  We are intentionally not packaging the latest
upstream (see Tim's message in the latest bug log[1]) and before I'll
check out this for the test case issue (and forward the issue to
upstream) I wonder whether somebody could confirm that we actually
could use the latest upstream as well.  Finally we will not manage
to stick to the old version for ever.

Kind regards

       Andreas.


[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802867#15

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