[pymvpa] macports install libsvm issue

[Grega Repovs]

Hi,

I just made a clean install of pyMVPA on Mac OS Leopard system using MacPorts:

sudo port install py26-pymvpa +scipy +pynifti +hcluster +libsvm +matplotlib +pywavelet

and separate installs of shogun and mdp:

sudo port install shogun +python26
sudo port install py26-mdp-toolkit

When trying to run the doc/examples/pylab_2d.py example I get the error: NameError: name 'LinearNuSVMC' is not defined

As suggested previously on the mailing list for the same issue on a Debian system I ran:

import mvpa
mvpa.base.externals.testAllDependencies(force=True)
mvpa.cfg

with results:

- - - -
>>> 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
>>> mvpa.base.externals.testAllDependencies(force=True)
WARNING: atlas_pymvpa is not available.
 * Please note: warnings are printed only once, but underlying problem might occur many times *
>>> mvpa.cfg
[externals]
have griddata = yes
have good scipy.stats.rdist = yes
have pylab plottable = yes
have pywt wp reconstruct = no
have ctypes = yes
have lxml = no
have running ipython env = no
have sg_fixedcachesize = yes
have reportlab = no
have shogun.mpd = yes
have matplotlib = yes
have pywt wp reconstruct fixed = no
have scipy = yes
have elasticnet = no
have openopt = no
have libsvm = no
have nifti ge 0.20090205.1 = yes
have weave = yes
have atlas_fsl = no
have mdp = yes
have hcluster = yes
have sg ge 0.6.4 = yes
have good scipy.stats.rv_discrete.ppf = yes
have libsvm verbosity control = no
have mdp ge 2.4 = yes
have shogun.svrlight = no
have rpy = no
have lars = no
have glmnet = no
have shogun = yes
have nifti = yes
have atlas_pymvpa = no
have cpickle = yes
have numpy = yes
have pylab = yes
have shogun.lightsvm = no
have pywt = yes
have gzip = yes

[general]
verbose = 1
- - -

Are there any suggestions how to get MacPorts package to install pyMVPA correctly with libsvm support? Also, I am wondering about the deprecation warnings for sets and matplotlib.numerix packages.

Thanks!

Grega