Hi
I compiled pytables on ubuntu 10 and although the usage example in the
py-tables documentation ( HowToUse ) works, the full tests launched with:
$ python -c 'import tables; tables.test()'
produces errors as shown in the attached file.
Note that the test suite of hdf5 itself passes, as well as the one
provided with h5py , another project using hdf5.
During a trac discussion ( ticket 308 ) it has been suggested, that
zlib is missing but I double-checked that it is there.
I has also been said that zlib must be compiled *within* hdf5 but I am
afraid I don't understand what that means.
Any ideas ?
Thanks
mycircuit
..............................................................................................................................................................................................................................................................................................................................................................................................................................F.F.....................F........HDF5-DIAG:
Error detected in HDF5 library version: 1.6.10 thread 0. Back trace follows.
#000: H5Dio.c line 601 in H5Dread(): can't read data
major(15): Dataset interface
minor(24): Read failed
#001: H5Dio.c line 866 in H5D_read(): can't read data
major(15): Dataset interface
minor(24): Read failed
#002: H5Dio.c line 1880 in H5D_chunk_read(): file gather failed
major(05): Low-level I/O layer
minor(24): Read failed
#003: H5Dselect.c line 205 in H5D_select_fgath(): read error
major(14): Dataspace interface
minor(24): Read failed
#004: H5Distore.c line 2060 in H5D_istore_readvv(): unable to read raw data
chunk
major(05): Low-level I/O layer
minor(24): Read failed
#005: H5Distore.c line 1564 in H5D_istore_lock(): data pipeline read failed
major(19): Data filters layer
minor(24): Read failed
#006: H5Z.c line 977 in H5Z_pipeline(): required filter is not registered
major(19): Data filters layer
minor(24): Read failed
E....................................................................................................................................................................................................................................................................................................................................................F......................F.............................................F......................F..................................................................................................................................................................................................FFF.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F....F..........................................................................F............................................................................................................................................................................................................F...............................................................................................................................F.....F...........................................................................................................................................................................................................FF.....FF...FF.....................................................................F.....................F..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
ERROR: None (tables.tests.test_backcompat.VLArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_backcompat.py",
line 113, in test01_backCompat
assert vlarray2[1] == ['5', '6', '77']
File "/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/vlarray.py",
line 617, in __getitem__
return self.read(start, stop, step)[0]
File "/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/vlarray.py",
line 752, in read
listarr = self._readArray(start, stop, step)
File "hdf5Extension.pyx", line 1539, in
tables.hdf5Extension.VLArray._readArray (tables/hdf5Extension.c:13309)
HDF5ExtError: VLArray._readArray: Problems reading the array data.
======================================================================
FAIL: None (tables.tests.test_create.FiltersCase1)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_create.py",
line 513, in test01_checkFilters
assert repr(gfilters) == repr(object_.filters)
AssertionError
======================================================================
FAIL: None (tables.tests.test_create.FiltersCase2)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_create.py",
line 513, in test01_checkFilters
assert repr(gfilters) == repr(object_.filters)
AssertionError
======================================================================
FAIL: Keeping filters when copying a file.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_create.py",
line 1365, in test01_copyFile
self._test_copyFile()
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_create.py",
line 1357, in _test_copyFile
self._check_filters(copyf, filters=filters)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_create.py",
line 1345, in _check_filters
"node ``%s`` should have filters" % node._v_pathname )
AssertionError: node ``/implicit_no/implicit_no/explicit_yes`` should have
filters
======================================================================
FAIL: None (tables.tests.test_tables.CompressZLIBTablesTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 1203, in test05_filtersTable
assert table.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.CompressZLIBShuffleTablesTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 1203, in test05_filtersTable
assert table.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.AllFiltersTablesTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 1203, in test05_filtersTable
assert table.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.CompressTwoTablesTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 1203, in test05_filtersTable
assert table.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.CloseCopyTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 4113, in test04_copy
assert 6 == table2.filters.complevel
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.CloseCopyTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 4184, in test05_copy
assert 6 == table2.filters.complevel
AssertionError
======================================================================
FAIL: None (tables.tests.test_tables.CloseCopyTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_tables.py",
line 4258, in test05b_copy
assert 6 == table2.filters.complevel
AssertionError
======================================================================
FAIL: None (tables.tests.test_earray.ZlibComprTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_earray.py",
line 181, in test01_iterEArray
assert earray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_earray.ZlibShuffleTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_earray.py",
line 181, in test01_iterEArray
assert earray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_earray.AllFiltersTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_earray.py",
line 181, in test01_iterEArray
assert earray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_vlarray.ZlibComprTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_vlarray.py",
line 127, in test01_read
assert vlarray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_vlarray.ShuffleComprTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_vlarray.py",
line 127, in test01_read
assert vlarray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: None (tables.tests.test_vlarray.AllFiltersTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_vlarray.py",
line 127, in test01_read
assert vlarray.filters.complevel == self.compress
AssertionError
======================================================================
FAIL: Reopening a file with tables using enumerated data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 226, in test00a_reopen
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: test00b_reopenMD (tables.tests.test_enum.EnumTableTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 242, in test00b_reopenMD
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: Reopening a file with extendable arrays using enumerated data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 403, in test00a_reopen
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: test00b_reopenMD (tables.tests.test_enum.EnumEArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 421, in test00b_reopenMD
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: Reopening a file with variable-length arrays using enumerated data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 503, in test00a_reopen
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: test00b_reopenMD (tables.tests.test_enum.EnumVLArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_enum.py",
line 521, in test00b_reopenMD
"Enumerated type was not restored correctly from disk.")
AssertionError: Enumerated type was not restored correctly from disk.
======================================================================
FAIL: Checking representation of a nested Table
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_nestedtypes.py",
line 701, in test00a_repr
""")
AssertionError
======================================================================
FAIL: test (tables.tests.test_hdf5compat.EnumTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/common.py",
line 248, in newmethod
return oldmethod(self, *args, **kwargs)
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_hdf5compat.py",
line 45, in test
self._test()
File
"/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/test_hdf5compat.py",
line 67, in _test
self.assertEqual(enum, expectedEnum)
AssertionError: Enum({'\x01': 0, '': 1, '\xb8\x1b&\n': 2, 'X\xbf\x83\nE': 3,
'\xe0\x7fH\nK': 4}) != Enum({'BLUE': 2, 'BLACK': 4, 'WHITE': 3, 'GREEN': 1,
'RED': 0})
----------------------------------------------------------------------
Ran 2942 tests in 71.621s
FAILED (failures=24, errors=1)
Closing remaining open files: /tmp/tmpWz7ixA.h5... done /tmp/tmpfoGNvZ.h5...
done
/usr/local/pytables-2.2/lib/python2.6/site-packages/tables/tests/flavored_vlarrays-format1.6.h5...
done /tmp/tmpP5tAiY.h5... done
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.2
HDF5 version: 1.6.10
NumPy version: 1.4.1
Numexpr version: 1.4.1 (not using Intel's VML/MKL)
Zlib version: 1.2.3.3 (in Python interpreter)
LZO version: 2.03 (Apr 30 2008)
BZIP2 version: 1.0.5 (10-Dec-2007)
Blosc version: 1.0 (2010-07-01)
Python version: 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
[GCC 4.4.3]
Platform: linux2-i686
Byte-ordering: little
Detected cores: 2
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 2 minutes to complete on a relatively
modern CPU and around 80 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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