[Numpy-discussion] Numpy installation problem

[Jonathan Tu]

On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:

> On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu <jhtu at princeton.edu> wrote:
> 
>> 
>> What does that part do?  It turns out that by fixing my library path, numpy now imports.  I assume that my installation of h5py doesn't need to be redone just because I reinstalled Numpy?
> 
> Actually, you may have to if you installed h5py against the numpy
> built from the trunk. I don't think the trunk ABI is forward
> compatible with 1.4.1,
> 
> David


Ok, so I reinstalled numpy as we've discussed, and now I've reinstalled h5py too.  When I test numpy, I get the following

import numpy
numpy.test()
Running unit tests for numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 326, in test
    self._show_system_info()
  File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 187, in _show_system_info
    nose = import_nose()
  File "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", line 69, in import_nose
    raise ImportError(msg)
ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose

Note that when I try test(level=1) it tells me this is an unexpected keyword argument.  (The level=1 was suggested by the scipy website.)  Though this test seems to fail, the simple math tests I've tried seem to work ok.

Then I tried to test h5py:
import h5py
import h5py.tests
h5py.tests.runtests()

======================================================================
ERROR: test_data (h5py.tests.test_filters.TestFilters)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", line 124, in test_data
    test_dset(s, t, compression=c, shuffle=False)
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", line 117, in test_dset
    dset[...] = arr
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/highlevel.py", line 1288, in __setitem__
    self.id.write(mspace, fspace, val, mtype)
  File "h5d.pyx", line 231, in h5py.h5d.DatasetID.write (h5py/h5d.c:2336)
  File "_proxy.pyx", line 115, in h5py._proxy.dset_rw (h5py/_proxy.c:1143)
TypeError: Not a dataset (Invalid arguments to routine: Inappropriate type)

======================================================================
FAIL: (File) Backing store for core driver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 135, in test_backing
    self.assert_('g' in self.f)
AssertionError

======================================================================
FAIL: (File) Append
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 52, in test_a
    self.assert_('g' in self.f)
AssertionError

======================================================================
FAIL: (File) Readwrite
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", line 72, in test_rp
    self.assert_('g' in self.f)
AssertionError

======================================================================
FAIL: test_open_close (h5py.tests.test_h5g.TestH5G)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_h5g.py", line 39, in test_open_close
    self.assert_(self.is_grp(grp))
AssertionError

----------------------------------------------------------------------
Ran 247 tests in 1.307s

FAILED (failures=4, errors=1)
<unittest._TextTestResult run=247 errors=1 failures=4>


But again, I seem to be able to open hdf5 files and look into them ok, though sometimes the files randomly close, i.e.

f = h5py.File( '/path/to/file.h5','r')
...
f
<Closed hdf5 file> (or something like this)

Should I be worried about these errors, or are things working ok?  Someone had once mentioned to me that the numpy tests are prone to failure.




Jonathan Tu