[pymvpa] MacOSX Installation

Matthias Zunhammer matthias.zunhammer at uk-essen.de
Thu Feb 26 13:35:05 UTC 2015

Hi all,

thank you for your help, after over a total of 8 hours of trying to install PyMVPA in vain, your helped me back on track. Thank you!

However, I urgently suggest that the PyMVPA-Developers update the installation section at http://www.pymvpa.org/installation.html <http://www.pymvpa.org/installation.html> for MacOSX. At this point it is not helpful (from my beginners perspective).

The problems in detail:
1.) The installation guide with the "Must Have“ and „Strong Recommendation“ sections in the beginning is misleading. New users (like me) will start downloading these packages (e.g. Anaconda), just to realize that the MacPorts routine below will do that automatically. This is a waste of time and memory and will lead to duplicate or triplicate versions of Python being installed... which in turn causes the PYTHONPATH-Problems I got stuck with.
2.) The first few installation steps for MacOSX work fine, but then the trouble begins:
3.) Installing Python and the necessary toolboxes with

sudo port install py25-pymvpa +scipy +nibabel +hcluster +libsvm +matplotlib +pywavelet

fails since the py-Version listed on the installation page is not up to date
(should be:
sudo port install py34-pymvpa +scipy +nibabel +hcluster +libsvm +matplotlib +pywavelet 

4.) The installation then stalls at first, because it requires SWIG (
sudo port install swig-python
, SWIG alone will not do!).
Swig is not mentioned in the Windows/Suse, but not in the MacOSX section of the installation guide.

5.) sudo port install python_select
runs without problems, but then neither
sudo python_select python25 (the version issue), nor sudo python_select python34 will not work.
Apparently the syntax has changed:

sudo port select python python34

Will do the job (see: http://stackoverflow.com/questions/6116697/macports-python-select-command-not-found).


> Am 25.02.2015 um 17:56 schrieb Christopher J Markiewicz <effigies at bu.edu>:
> On 02/25/2015 11:31 AM, Matthias Zunhammer wrote:
>> Hi,
>> I succeeded to install pyMVPA on MacOSX, but after starting python and
>> typing
>>>> import mvpa2
>> I get the following error:
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>> ImportError: No module named mvpa2
> Likely it's not in your PYTHONPATH.
> Find your installation:
> sudo updatedb && locate mvpa2/__init__.py
> Mine is: /usr/lib/python2.7/dist-packages/mvpa2/__init__.py, so I want
> to make sure /usr/lib/python2.7/dist-packages is in my python path.
> Examine your path:
> python -c 'import sys; print sys.path'
> If your directory isn't in there, you can add it with a command like this:
> echo 'PYTHONPATH=$PYTHONPATH:/usr/lib/python2.7/dist-packages' >> ~/.bashrc
> The single quotes are important. Obviously use the directory you found
> above, and if you're not using bash, you may need to append the line to
> a different RC file than ~/.bashrc.
> Hope this helps.
> -- 
> Christopher J Markiewicz
> Ph.D. Candidate, Quantitative Neuroscience Laboratory
> Boston University
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Dr. phil. Matthias Zunhammer
M.Sc. Neurowissenschaften 

Universitätsklinikum Essen (AöR)
Klinik für Neurologie
Gebäude OZ I, Raum 10.4.013
Hufelandstraße 55
D-45147 Essen
Telefon +49 176 / 60016738
Fax +49 201 / 723-6882
E-Mail: matthias.zunhammer at uk-essen.de

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