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

Adam Schneider amschne@umich....
Thu Dec 27 15:09:20 CST 2012


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

Thanks again,

Adam


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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