[SciPy-User] numpy.test() fail mac with homebrew python 2.7

Ralf Gommers ralf.gommers@gmail....
Thu Dec 27 15:39:33 CST 2012


On Thu, Dec 27, 2012 at 10:09 PM, Adam Schneider <amschne@umich.edu> wrote:

> Hey Ralf, thanks for the quick response.
>
> I tried a clean install, but scipy still fails to install with this error:
> numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s)
> ['/usr/local/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini']
>
> It looks like it is the same issue that people are running into here:
> http://stackoverflow.com/questions/12574604/scipy-install-on-mountain-lion-failing
>
> Trying the workaround suggested on SO and installing numpy from top of
> tree allows scipy to install from pip, but numpy.test() fails the following
> test:
>
> FAIL: Test numpy dot with different order C, F
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in
> runTest
>     self.test(*self.arg)
>   File
> "/usr/local/lib/python2.7/site-packages/numpy/core/tests/test_blasdot.py",
> line 119, in test_dot_array_order
>     assert_array_equal(a.dot(a_T), a.dot(a.T))
>   File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 719, in assert_array_equal
>     verbose=verbose, header='Arrays are not equal')
>   File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py",
> line 645, in assert_array_compare
>     raise AssertionError(msg)
> AssertionError:
> Arrays are not equal
>
> (mismatch 11.0%)
>  x: array([[  8.33980975,  -1.73402744,   8.39918067,  -0.92846214,
>          -1.42408847,   3.07286699,   2.08420574,  -0.48730198,
>           0.1639567 ,  -1.04598212],...
>  y: array([[  8.33980975,  -1.73402744,   8.39918067,  -0.92846214,
>          -1.42408847,   3.07286699,   2.08420574,  -0.48730198,
>           0.1639567 ,  -1.04598212],...
>
> ----------------------------------------------------------------------
> Ran 4801 tests in 18.344s
>
> FAILED (KNOWNFAIL=5, SKIP=5, failures=1)
> <nose.result.TextTestResult run=4801 errors=0 failures=1>
>
> Should this be a known fail?
>

No, it shouldn't. Doesn't look serious but should be fixed. Could you open
an issue on Github, and list the compilers and build command used?


> Also, should scipy from pip (0.11.0) install cleanly with numpy from pip
> (1.6.2)?
>

It should, but apparently it's broken in a not very reproducible way.
That's going to take some time to fix probably. This sort of thing is why I
usually avoid pip & co by the way.

Ralf


> On Thu, Dec 27, 2012 at 12:17 PM, Jordan Schneider <jbschne@umich.edu>wrote:
>
>>
>>
>> Sent from my iPad
>>
>> Begin forwarded message:
>>
>> *From:* Ralf Gommers <ralf.gommers@gmail.com>
>> *Date:* December 27, 2012, 2:37:47 PM EST
>> *To:* SciPy Users List <scipy-user@scipy.org>
>> *Cc:* Jordan Schneider <jbschne@umich.edu>
>> *Subject:* *Re: [SciPy-User] numpy.test() fail mac with homebrew python
>> 2.7*
>>
>>
>>
>>
>> On Wed, Dec 26, 2012 at 9:31 PM, Adam Schneider <amschne@umich.edu>wrote:
>>
>>> After installing numpy version 1.6.2 and scipy version 0.11.0 via pip
>>> 1.2.1 for python 2.7.3 (from homebrew) on my MacBook Air with core i7
>>> processors on OS X 10.8.2, I ran tests using numpy.test() and scipy.test()
>>> which both failed.  Below are three failure lines from the numpy.test, and
>>> attached is the full log.
>>>
>>> FAIL: Test automatically generated assignments which overlap in memory.
>>> FAIL: test_nditer.test_iter_broadcasting_errors
>>> FAIL: test_nditer.test_iter_array_cast
>>>
>>> Will you please let me know how big of an issue this is and the best way
>>> to fix it?
>>>
>>
>> Hi Adam,
>>
>> It looks like all the errors come from files left over from a previous
>> numpy install. The basis and cast methods were added in 1.7.x.
>>
>> An "rm -rf numpy/" and clean reinstall should fix it.
>>
>> Ralf
>>
>>
>
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