[pymvpa] problem installing PyMVPA on ubuntu

[Scott Gorlin]

i wonder if shogun is installed correctly.  looking closer at your 
error, looks like it's looking for a lapack library.  have you installed 
lapack and all those goodies?

if you need shogun, i'd highly recommend installing the version from 
shogun-toolbox.org, which is many versions newer than ubuntu's.  that 
should also take care of any dependencies it requires like lapack.

do the libsvm backend classifiers work?  if not then it may be that your 
libsvm installation didn't take for some reason, which is why it's 
trying to import from shogun (can't recall off the top of my head 
whether mvpa.suite will import the shogun libraries if libsvm isn't 
installed).

there's also a workaround to prevent loading shogun even if it's 
installed.  you shouldn't have needed this unless you actually had it 
installed previously, so I'm a bit confused why you're getting this 
error.   however, prior to importing suite, try this:

import mvpa.base.externals
mvpa.base.externals._VERIFIED['shogun'] = False

from mvpa.suite import *

Greg Detre wrote:
> thanks for the tip.
>
> i tried this:
>
> sudo aptitude install shogun-python shogun-python-modular
> sudo apt-get install libsvm2 python-libsvm
>
> still no dice.
>
> g
>
>
> Scott Gorlin wrote:
>>  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
>> >
>> >
>> > _______________________________________________ Pkg-ExpPsy-PyMVPA
>> > mailing list Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
>> > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
>
>