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

Wed Oct 31 04:29:15 EDT 2012

On Sat, Oct 27, 2012 at 5:16 PM, Virgil Stokes <vs at it.uu.se> wrote:

>  On 27-Oct-2012 09:44, Ralf Gommers wrote:
>
>
>
> On Fri, Oct 26, 2012 at 10:15 PM, David Warde-Farley <
> wardefar at 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 at 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?
>> > _______________________________________________
>> > SciPy-User mailing list
>> > SciPy-User at scipy.org
>> > http://mail.scipy.org/mailman/listinfo/scipy-user
>> _______________________________________________
>> SciPy-User mailing list
>> SciPy-User at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-user
>>
>
>
>
> _______________________________________________
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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!
>

The installer byte-compiles the Python code during install, for which it
uses the Python it picks up from the Windows registry. I don't know all
that much about bdist_wininst, but I think that just making the install
path editable is going to work. Where do you get your Python for
byte-compiling for then, just scan all subdirs for a python.exe file?

The installer that bdist_wininst creates simply isn't made for using
non-default Pythons it looks like.

> 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,
>

A simple shortcut is to copy the site-packages/numpy/ dir from C:/ to D:/.

> >>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.
>

That's OK indeed.

Ralf
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