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

[Adam Schneider]

Thanks for the help. numpy 1.7.0b2 and 1.6.2 are passing tests. I filed an
issue for 1.8.0.dev-a8c641f: https://github.com/numpy/numpy/issues/2860

However, scipy 0.11.0 and top of tree (0.12.0.dev-b69fe18) are not passing
tests (installing directly from distutils and from pip). Attached is the
output from 0.11.0 tests (72 failures). Any idea why this might be
happening?

Thanks,
Adam


On Thu, Dec 27, 2012 at 1:39 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:

>
>
>
> On Thu, Dec 27, 2012 at 10:09 PM, Adam Schneider <amschne at 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 at umich.edu>wrote:
>>
>>>
>>>
>>> Sent from my iPad
>>>
>>> Begin forwarded message:
>>>
>>> *From:* Ralf Gommers <ralf.gommers at gmail.com>
>>> *Date:* December 27, 2012, 2:37:47 PM EST
>>> *To:* SciPy Users List <scipy-user at scipy.org>
>>> *Cc:* Jordan Schneider <jbschne at 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 at 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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