Warnings --- why do they occur and how can I stop them?

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Warnings --- why do they occur and how can I stop them?

Virgil Stokes
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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Re: Warnings --- why do they occur and how can I stop them?

David Warde-Farley-3
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.

On Fri, Oct 26, 2012 at 1:57 PM, Virgil Stokes <[hidden email]> 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
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-user
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Re: Warnings --- why do they occur and how can I stop them?

ralfgommers


On Fri, Oct 26, 2012 at 10:15 PM, David Warde-Farley <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-user
_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user


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Re: Warnings --- why do they occur and how can I stop them?

Virgil Stokes
On 27-Oct-2012 09:44, Ralf Gommers wrote:


On Fri, Oct 26, 2012 at 10:15 PM, David Warde-Farley <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-user
_______________________________________________
SciPy-User mailing list
[hidden email]
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!

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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Re: Warnings --- why do they occur and how can I stop them?

Virgil Stokes
In reply to this post by David Warde-Farley-3
On 26-Oct-2012 22:15, David Warde-Farley 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.
>
> On Fri, Oct 26, 2012 at 1:57 PM, Virgil Stokes <[hidden email]> 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
>> [hidden email]
>> http://mail.scipy.org/mailman/listinfo/scipy-user
> _______________________________________________
> SciPy-User mailing list
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-user
Thanks for you help,

I have now fixed the problem (see my response that was posted earlier).

--V
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Re: Warnings --- why do they occur and how can I stop them?

ralfgommers
In reply to this post by Virgil Stokes


On Sat, Oct 27, 2012 at 5:16 PM, Virgil Stokes <[hidden email]> wrote:
On 27-Oct-2012 09:44, Ralf Gommers wrote:


On Fri, Oct 26, 2012 at 10:15 PM, David Warde-Farley <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/scipy-user
_______________________________________________
SciPy-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user



_______________________________________________
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[hidden email]
http://mail.scipy.org/mailman/listinfo/scipy-user
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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