[SciPy-User] Warnings --- why do they occur and how can I stop them?

Virgil Stokes vs@it.uu...
Sat Oct 27 10:16:02 CDT 2012


On 27-Oct-2012 09:44, Ralf Gommers wrote:
>
>
> On Fri, Oct 26, 2012 at 10:15 PM, David Warde-Farley 
> <wardefar@iro.umontreal.ca <mailto:wardefar@iro.umontreal.ca>> wrote:
>
>     It sounds as if you've installed a binary-incompatible version of
>     SciPy for the version of NumPy that you have.
>
>     SciPy's version requirements are pretty loose but since SciPy if
>     you're installing binaries, you need to be sure that the SciPy binary
>     you get was compiled against the same version of NumPy that you get
>     (or at least one with the same ABI version, to get technical).
>
>     Deleting whatever you currently have and downloading one of the
>     "superpack" installers from here
>     http://sourceforge.net/projects/scipy/files/scipy/0.11.0/ should fix
>     you up.
>
>
>  That's not necessary. If
>     >>> import scipy
>     >>> scipy.test()
>  runs without issues the install works fine.
>
> The reason for these warnings is Cython being too picky, they can be silenced 
> like in: https://github.com/numpy/numpy/pull/432
>
> Ralf
>
>     On Fri, Oct 26, 2012 at 1:57 PM, Virgil Stokes <vs@it.uu.se
>     <mailto:vs@it.uu.se>> wrote:
>     > I have the following installed:
>     >
>     >    NumPy 1.6.1
>     >    SciPy 0.11.0
>     >
>     > on a Windows Vista (32-bit) platform with Python 2.7
>     >
>     > I get the following warnings:
>     >
>     > D:\python27\lib\site-packages\scipy\io\matlab\mio4.py:15: RuntimeWarning:
>     > numpy.dtype size changed, may indicate binary incompatibility
>     >        from mio_utils import squeeze_element, chars_to_strings
>     > D:\python27\lib\site-packages\scipy\io\matlab\mio4.py:15: RuntimeWarning:
>     > numpy.ufunc size changed, may indicate binary incompatibility
>     >        from mio_utils import squeeze_element, chars_to_strings
>     > D:\python27\lib\site-packages\scipy\io\matlab\mio5.py:96: RuntimeWarning:
>     > numpy.dtype size changed, may indicate binary incompatibility
>     >        from mio5_utils import VarReader5
>     > D:\python27\lib\site-packages\scipy\io\matlab\mio5.py:96: RuntimeWarning:
>     > numpy.ufunc size changed, may indicate binary incompatibility
>     >        from mio5_utils import VarReader5
>     >
>     >   When the following statement is executed
>     >
>     > from scipy import io
>     >
>     > Why does this occur and what can be done to fix this problem?
>     > _______________________________________________
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>     > SciPy-User@scipy.org <mailto:SciPy-User@scipy.org>
>     > http://mail.scipy.org/mailman/listinfo/scipy-user
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>
>
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Ok Ralf,
Your suggestion led me to find the source of the problem and to make some 
changes to my system configuration
Here is a short summary:

I have python 2.6, 2.7, 3.3 installed on C:\ and D:\

The problem that I experienced was with 2.7 on D:\

Unfortunately when installing SciPy from the binary

scipy-0.11.0-win32-superpack-python2.7.exe

During the installation it finds (from the system path) that I have python 2.7 
installed on C:\
and this is indicated in the installation; however, it does not allow one to 
edit (change) this to D:\

IMHO this should be fixed --- why even show this information and set the cursor 
for editing but not allow one to actually edit anything!

After a lot of manipulation of the system path with drive changes, I finally 
decided to work with my installation on C:\, and now taking your suggestion,

 >>import sys
 >>scipy.test()
Running unit tests for scipy
NumPy version 1.6.2
NumPy is installed in c:\Python27\lib\site-packages\numpy
SciPy version 0.11.0
SciPy is installed in c:\Python27\lib\site-packages\scipy
Python version 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)]
nose version 1.1.2
..............................................................................................................................................................................................................................K........................................................................................................K..................................................................K..K....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS...............................................................................S.........K...................................................................................................................................................................................................................................................................................K.........................................................................................................................................................................................................................K...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K..................................................................K................................................................................................................................................................KK..............................................................................................................................................................................................................................................................................................................................................................................................................................c:\Python27\lib\site-packages\scipy\special\tests\test_basic.py:1606: 
RuntimeWarning: invalid value encountered in absolute
   assert_(np.abs(c2) >= 1e300, (v, z))
.........................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS............................................................................................................................................................................S..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 5488 tests in 54.906s

OK (KNOWNFAIL=15, SKIP=36)
<nose.result.TextTestResult run=5488 errors=0 failures=0>

which is not very elegant; but, I believe ok.

Again, why can one not edit the installation drive for SciPy when installing 
from the binary?

Thanks for your help.

--V
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