[pymvpa] Trouble running pyMVPA on Mac OS 10.6.6

[Thad Polk]

On Wed, 26 Oct 2011, Yaroslav Halchenko wrote:

> 1. try installing/using it directly from sources: it should be as simple as
>
>  git clone git://github.com/PyMVPA/PyMVPA.git
>  cd PyMVPA
>  make
>  export PYTHONPATH=$PWD
>
> and you should be all set

This did indeed solve my initial problem (thanks). But now it complains 
about nibabel:

lip_osx_157_251:~ guest$ python
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> from mvpa2.tutorial_suite import *

>>> ds = get_haxby2001_data()
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/Users/guest/PyMVPA/mvpa2/tutorial_suite.py", line 42, in 
get_haxby2001_data
     ds = get_raw_haxby2001_data(roi=roi)
   File "/Users/guest/PyMVPA/mvpa2/tutorial_suite.py", line 37, in 
get_raw_haxby2001_data
     return load_datadb_tutorial_data(path=path, roi=roi)
   File "/Users/guest/PyMVPA/mvpa2/misc/data_generators.py", line 354, in 
load_datadb_tutorial_data
     import nibabel as nb
ImportError: No module named nibabel


The output from mvpa2.wtf() below indicates that I'm missing a number of 
externals, including nibabel.  More thoughts?

Thanks,

Thad



>>> mvpa2.wtf()
Current date:   2011-10-26 15:36
PyMVPA:
  Version:       2.0.0~rc5
  Hash:          $Format:%H$
  Path:          /Users/guest/PyMVPA/mvpa2/__init__.pyc
  Version control (GIT):
   Status:
    # On branch master
    # Untracked files:
    #   (use "git add <file>..." to include in what will be committed)
    #
    #	mvpa2/clfs/libsvmc/svmc.py
    nothing added to commit but untracked files present (use "git add" to 
track)
   Reference:
    d96dea8c74168e34217600d22879b614927732de HEAD
    d96dea8c74168e34217600d22879b614927732de refs/remotes/origin/HEAD
   Difference from last release 2.0.0~rc5:
    fatal: ambiguous argument 'upstream/2.0.0~rc5...': unknown revision or 
path not in the working tree.
    Use '--' to separate paths from revisions
SYSTEM:
  OS:            posix Darwin 10.6.0 Darwin Kernel Version 10.6.0: Wed Nov 
10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386
  Distribution:   10.6.6/i386
EXTERNALS:
  Present:       cPickle, ctypes, gzip, libsvm, libsvm verbosity control, 
numpy
  Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good 
scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, h5py, 
hcluster, lars, lxml, mass, matplotlib, mdp, mdp ge 2.4, nibabel, nipy, 
nipy.neurospin, nose, openopt, pprocess, pylab, pylab plottable, pywt, 
pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy2, running 
ipython env, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, 
shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight, 
skl, weave
  Versions of critical externals:
   numpy       : 1.2.1
   ctypes      : 1.1.0
   nifti       : failed to query due to "nifti is not a known dependency 
key."
   numpy       : 1.2.1
RUNTIME:
  PyMVPA Environment Variables:
   PYTHONPATH          : "/Users/guest/PyMVPA"
  PyMVPA Runtime Configuration:
   [externals]
   have griddata = no
   have pprocess = no
   have good scipy.stats.rdist = no
   have pylab plottable = no
   have pywt wp reconstruct = no
   have pywt = no
   have lxml = no
   have running ipython env = no
   have nibabel = no
   have ctypes = yes
   have sg_fixedcachesize = no
   have elasticnet = no
   have shogun.mpd = no
   have matplotlib = no
   have pywt wp reconstruct fixed = no
   have scipy = no
   have reportlab = no
   have openopt = no
   have libsvm = yes
   have nose = no
   have weave = no
   have atlas_fsl = no
   have h5py = no
   have hcluster = no
   have sg ge 0.6.4 = no
   have sg ge 0.6.5 = no
   have good scipy.stats.rv_discrete.ppf = no
   have skl = no
   have mdp ge 2.4 = no
   have shogun.svrlight = no
   have lars = no
   have shogun.svmocas = no
   have nipy = no
   have glmnet = no
   have mass = no
   have shogun = no
   have libsvm verbosity control = yes
   have shogun.krr = no
   have atlas_pymvpa = no
   have cpickle = yes
   have mdp = no
   have numpy = yes
   have pylab = no
   have rpy2 = no
   have shogun.lightsvm = no
   have gzip = yes
   have nipy.neurospin = no

   [general]
   verbose = 1

>>>