[pymvpa] Problem installing on Mac OS X #shogun26vs25 #deprecation warning

[Christian Fiebach]

Dear all,

a brief update, just in case this might help others:

I managed to install py25-pymvpa under leopard finally.


#shogun:
It appears that the current version of shogun in MacPorts (i.e., 0.9)  
is dependent on
python26, which caused MacPorts to additionally install python26 (see  
earlier mail in the
thread). This can be suppressed by installing shogun in the following  
way:

sudo port -v install shogun +no_python26 +python25

which makes installation of py25-pymvpa (sudo port install py25- 
pymvpa) possible.


#Deprecation warning: Some problems seem to persist:

 >>> from mvpa.suite import *
/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/matplotlib/numerix/__init__.py:18:  
DeprecationWarning:
**********************************************************
matplotlib.numerix and all its subpackages are deprecated.
They will be removed soon.  Please use numpy instead.
**********************************************************

   warnings.warn(msg, DeprecationWarning)


Best, Christian


Am 10.12.2009 um 17:13 schrieb Christian Fiebach:

> Thanks Anna,
>
> installing as you suggested fully using py26 worked, with your  
> commands given below. Thanks!!!
>
> However, my first steps in pyMVPA continue to be difficult:
>
> When I start python and try to follow the installation website or  
> the getting started manual,
> python produces either error messages or crashes:
>
> From the installation web site: Deprecation Warning @ import and  
> NameError for the very first command.
>
> fiebach$ python
> Python 2.6.4 (r264:75706, Dec  8 2009, 01:05:52)
> [GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import mvpa
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/site-packages/mvpa/base/verbosity.py:19:  
> DeprecationWarning: the sets module is deprecated
>   from sets import Set
> >>> attr = SampleAttributes(os.path.join(pymvpa_dataroot,  
> 'attributes.txt'))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> NameError: name 'SampleAttributes' is not defined
> >>>
>
>
> From the Getting Started section of the Manual: Deprecatin error and  
> python crash
>
> fiebach$ python
> Python 2.6.4 (r264:75706, Dec  8 2009, 01:05:52)
> [GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from mvpa.suite import *
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/site-packages/mvpa/base/verbosity.py:19:  
> DeprecationWarning: the sets module is deprecated
>   from sets import Set
> Python(673) malloc: *** error for object 0x7fff70e8b500: pointer  
> being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap
> fiebach$
>
>
> Just to make sure: My path seems to look fine. The export command is  
> currently in .profile,
> not in .bash_profile as suggested in the installation section:
>
> fiebach$ echo $PATH
> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/ 
> local/bin:/usr/X11/bin
>
>
>
> Unfortunately, I am just starting to use python and therefore my  
> debugging abilities
> are not very advanced at present. I am greatful for any input you  
> can give me right
> now!
>
> Thanks in advance,
>
> Christian
>
>
> Am 08.12.2009 um 14:57 schrieb Anna Manelis:
>
>> Christian,
>> I am not an expert, but I managed to install PYMVPA on my Snow  
>> Leopard by doing
>> sudo port install py26-pil py26-numpy py26-scipy py26-ipython py26- 
>> matplotlib +cairo+latex+tkinter  py26-pyobjc2-cocoa python_select
>> sudo python_select python26
>> And then
>> sudo port install py26-pymvpa +scipy +pynifti +hcluster +libsvm  
>> +matplotlib +pywavelet
>> Although when I tried to install PYMVPA on Leopard, I encountered  
>> the same problem as you (the installation involves py26 even though  
>> I explicitly aske it to involve py25).
>>
>> Good luck,
>> Anna.
>>
>
>
>
>
>
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-------------------------------------------------------------
Prof. Dr. Christian Fiebach
Dept. of Psychology, University of Heidelberg
Hauptstr. 47-51; D-69117 Germany
Tel.: ++49-(0)6221-547371
http://fimlab.uni-hd.de
-------------------------------------------------------------




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