HDF5 libraries fail test suites on Windows, h5py, PyTables

[mrocklin]

On a windows machine with anaconda installed neither of the h5py nor pytables libraries pass their test suites.

This came from @mwiebe 's development system

import h5py
h5py.run_tests()

import tables
tables.test()

h5py

FAILED (failures=34, errors=19, skipped=18, expected failures=1)

PyTables

======================================================================
ERROR: test05b_modifyColumns (tables.tests.test_nestedtypes.WriteNoReopen)
Modifying two nested columns (modify_columns).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\tests\common.py", line 154, in newmethod
    return oldmethod(self, *args, **kwargs)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\tests\test_nestedtypes.py", line 531, in test05b_modifyColumns
    dtype=raCols.dtype)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\records.py", line 519, in fromarrays
    arrayList = [sb.asarray(x) for x in arrayList]
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\records.py", line 519, in <listcomp>
    arrayList = [sb.asarray(x) for x in arrayList]
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\numeric.py", line 460, in asarray
    return array(a, dtype, copy=False, order=order)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 3501, in __iter__
    out=buf_slice)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 1930, in read
    arr = self._read(start, stop, step, field, out)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 1834, in _read
    bytes_required))
ValueError: output array size invalid, got 8 bytes, need 16 bytes

======================================================================
ERROR: test05b_modifyColumns (tables.tests.test_nestedtypes.WriteReopen)
Modifying two nested columns (modify_columns).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\tests\common.py", line 154, in newmethod
    return oldmethod(self, *args, **kwargs)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\tests\test_nestedtypes.py", line 531, in test05b_modifyColumns
    dtype=raCols.dtype)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\records.py", line 519, in fromarrays
    arrayList = [sb.asarray(x) for x in arrayList]
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\records.py", line 519, in <listcomp>
    arrayList = [sb.asarray(x) for x in arrayList]
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\numpy\core\numeric.py", line 460, in asarray
    return array(a, dtype, copy=False, order=order)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 3501, in __iter__
    out=buf_slice)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 1930, in read
    arr = self._read(start, stop, step, field, out)
  File "C:\Users\mwiebe\Anaconda\lib\site-packages\tables\table.py", line 1834, in _read
    bytes_required))
ValueError: output array size invalid, got 8 bytes, need 16 bytes

----------------------------------------------------------------------
Ran 5392 tests in 258.395s

FAILED (errors=2)

[groutr]

I get failures with pytables only on my windows system. The test cases are complaining that they can't create hdf5 files for the test.

[wavetossed]

I got the same errors on OSX running the PYTables test using the Anaconda distro of Python, i.e.

export PATH="/opt/anaconda/bin:$PATH" python Python 2.7.9 |Anaconda 2.2.0 (x86_64)| (default, Dec 15 2014, 10:37:34) [GCC 4.2.1 (Apple Inc. build 5577)] on darwin blah blah ...

import tables tables.test

This is a Macbook running the latest OSX Yosemite Given that Macs are more uniform one to another, you might want to borrow a Yosemite Macbook and run this the Anaconda Python distro to track down where it is coming from.

P.S. possible red herring, but I installed Anaconda because I was unable to build PYTables using

pip install tables on my regular Python which was 2.7 installed from MacPorts. Something to do with globals,h (originating from BSD/GCC) and a config.h Possibly something to do with glib2

[goanpeca]

Closing for lack of activity.

Please reopen if this is still a problem with an update of the status.

Thanks!