[Numpy-discussion] Numpy installation problem

Keith Goodman kwgoodman@gmail....
Sat Jul 24 17:51:33 CDT 2010


On Sat, Jul 24, 2010 at 3:39 PM, Jonathan Tu <jhtu@princeton.edu> wrote:
>
> On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
>
>> On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu <jhtu@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.
>
>

Yes, you should be worried. To run the numpy tests you need to install
nose. That's what your output said:

ImportError: Need nose >= 0.10.0 for tests - see
http://somethingaboutorange.com/mrl/projects/nose

For h5py, you might want to try the h5py list. Did you remove the
build directory? Because I don't know much about installation, I
remove everything: the installed package, the build directory.


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