[pymvpa] Recursive Feature Elimination errors

[Mike E. Klein]

Hi Michael,

Thanks so much for the help! Output is below.

Best,
Mike

In [2]: mvpa.wtf()
/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/nose/util.py:14:
DeprecationWarning: The compiler package is deprecated and removed in Python
3.x.
  from compiler.consts import CO_GENERATOR
Out[2]:
Current date:   2011-10-11 10:10
PyMVPA:
 Version:       0.6.0~rc3
 Hash:          fd0f2809300cc25e81ee21a3a876d00d524402c1
 Path:
 /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/mvpa/..
is not under GIT"
SYSTEM:
 OS:            posix Darwin 11.0.1 Darwin Kernel Version 11.0.1: Thu Jul 28
02:01:39 PDT 2011; root:xnu-1699.23.4~1/RELEASE_X86_64
 Distribution:   10.7.1/x86_64
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, libsvm, libsvm verbosity
control, lxml, matplotlib, mdp, mdp ge 2.4, nibabel, nose, numpy, pylab,
pylab plottable, reportlab, scipy, skl, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, hcluster, lars,
mass, nipy, nipy.neurospin, openopt, pprocess, pywt, pywt wp reconstruct,
pywt wp reconstruct fixed, rpy2, running ipython env, sg ge 0.6.4, sg ge
0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd,
shogun.svmocas, shogun.svrlight
 Versions of critical externals:
  nibabel     : 1.2.0.dev
  reportlab   : 2.5
  matplotlib  : 1.0.1
  scipy       : 0.9.0
  skl         : 0.8
  mdp         : 3.1
  numpy       : 1.6.0
  ctypes      : 1.1.0
  matplotlib  : 1.0.1
  lxml        : 2.3.0
  nifti       : failed to query due to "nifti is not a known dependency
key."
  numpy       : 1.6.0
 Matplotlib backend: MacOSX
RUNTIME:
 PyMVPA Environment Variables:
   PyMVPA Runtime Configuration:
  [general]
  verbose = 1

  [externals]
  have running ipython env = no
  have numpy = yes
  have scipy = yes
  have matplotlib = yes
  have lxml = yes
  have nibabel = yes
  have atlas_fsl = no
  have atlas_pymvpa = no
  have cpickle = yes
  have ctypes = yes
  have elasticnet = no
  have glmnet = no
  have good scipy.stats.rdist = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have griddata = yes
  have gzip = yes
  have h5py = yes
  have hcluster = no
  have lars = no
  have pylab = yes
  have libsvm = yes
  have libsvm verbosity control = yes
  have mass = no
  have mdp = yes
  have mdp ge 2.4 = yes
  have nipy = no
  have nipy.neurospin = no
  have nose = yes
  have openopt = no
  have pprocess = no
  have pylab plottable = yes
  have pywt = no
  have pywt wp reconstruct = no
  have pywt wp reconstruct fixed = no
  have reportlab = yes
  have rpy2 = no
  have sg ge 0.6.4 = no
  have sg ge 0.6.5 = no
  have sg_fixedcachesize = no
  have shogun = no
  have shogun.krr = no
  have shogun.lightsvm = no
  have shogun.mpd = no
  have shogun.svmocas = no
  have shogun.svrlight = no
  have skl = yes
  have weave = yes


On Mon, Oct 10, 2011 at 3:55 AM, Michael Hanke <mih at debian.org> wrote:

> Hey,
>
> On Sat, Oct 08, 2011 at 01:35:06PM -0400, Mike E. Klein wrote:
> > Just wondering if anyone had any advice on this… I'm pretty hopelessly
> stuck
> > and would love to be able to do this RFE-based analysis.
>
> Sorry for the delay and the versioning mess. Before I can say anthing
> about the proper RFE code, we need to figure out what PyMVPA you are
> actually running. Can you please post the output of
>
>  >>> import mvpa
>  >>> mvpa.wtf()
>
> That should get us started. If you get an error with 'import mvpa',
> please test 'import mvpa2' as you may run very recent code.
>
> Thanks,
>
> Michael
>
> --
> Michael Hanke
> http://mih.voxindeserto.de
>
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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