[pymvpa] problem installing PyMVPA on ubuntu

[Scott Gorlin]

do you have libsvm installed?

sudo apt-get install libsvm2 (i think)

it looks like it's trying to load Shogun instead of libsvm.  
Alternatively, you could install shogun.

i run mvpa on ubuntu just fine, though I don't recall when I switched 
from the packages to the git repositories

Greg Detre wrote:
> hey you guys,
>
> per & i were playing with a direct comparison of PyMVPA and the matlab 
> MVPA toolbox, just to confirm that they gave similar results when fed 
> identical data.
>
> anyway, i've been having trouble getting it to work on an ubuntu 
> machine in the lab, and wanted to give you a heads-up.
>
> Ubuntu Intrepid 8.10
> Linux gyruss 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 
> x86_64 GNU/Linux
>
> per had suggested i use the latest version from michael's top-secret 
> underground repository:
>
> http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/debian&lang=en 
>
>
> [i haven't tried the official intrepid repository version]
>
> # this is what i added to /etc/apt/sources.list
> deb http://apsy.gse.uni-magdeburg.de/debian intrepid main
> # i didn't bother adding the key
>
> sudo apt-get update
>
> installed python-mvpa
>
> i can run 'import mvpa' just fine. but if i try 'from mvpa.suite 
> import *', i get the error pasted below
>
> just wanted to let you know,
>
> g
>
>
> --------------------------------------------------------------------------- 
>
> ImportError                               Traceback (most recent call 
> last)
>
> /qbert/home/greg/<ipython console> in <module>()
>
> /var/lib/python-support/python2.5/mvpa/suite.py in <module>()
>      43 from mvpa.clfs.stats import *
>      44 if externals.exists('libsvm') or externals.exists('shogun'):
> ---> 45     from mvpa.clfs.svm import *
>      46 from mvpa.clfs.transerror import *
>      47 from mvpa.clfs.warehouse import *
>
> /var/lib/python-support/python2.5/mvpa/clfs/svm.py in <module>()
>      52
>      53 if externals.exists('shogun'):
> ---> 54     from mvpa.clfs import sg
>      55     SVM = sg.SVM
>      56     #if not 'LinearCSVMC' in locals():
>
> /var/lib/python-support/python2.5/mvpa/clfs/sg/__init__.py in <module>()
>      15     debug('INIT', 'mvpa.clfs.sg')
>      16
> ---> 17 from mvpa.clfs.sg.svm import SVM
>      18
>      19 if __debug__:
>
> /var/lib/python-support/python2.5/mvpa/clfs/sg/svm.py in <module>()
>      27 # Rely on SG
>      28 import shogun.Features
> ---> 29 import shogun.Classifier
>      30 import shogun.Regression
>      31 import shogun.Kernel
>
> /usr/lib/python2.5/site-packages/shogun/Classifier.py in <module>()
>       9 """
>      10
> ---> 11 import _Classifier
>      12 import new
>      13 new_instancemethod = new.instancemethod
>
> ImportError: /usr/lib/python2.5/site-packages/shogun/_Classifier.so: 
> undefined symbol: clapack_dpotrf
>
>
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