[pymvpa] macports install libsvm issue

James Kyle jameskyle at ucla.edu
Tue Dec 1 17:50:33 UTC 2009


I'm seeing the same thing. 

I'll look into it.

-james
On Nov 27, 2009, at 11:11 PM, Grega Repovs wrote:

> 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
> 
> 
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