[pymvpa] pymvpa installation problem... nifti not found

tbeck at artsci.wustl.edu tbeck at artsci.wustl.edu
Fri Oct 29 17:08:37 UTC 2010

hey Yaroslav

Thanks for getting back to me so quickly.

python -c 'import nifti' gave me the same error:
Import Error: No module named nifti

When I ran print mvpa.wtf(), I noticed a bunch of the externals don't seem
to have installed properly (see below).  Is there a command to install
these individually manually?  can you tell from this output what may have
gone wrong?  Thanks much in advance for any help you can offer!


DeprecationWarning: the sets module is deprecated
  from sets import Set
Current date:   2010-10-29 12:01
 Version:       0.4.5.dev
 Version control (GIT):
 GIT information could not be obtained due
is not under GIT"
 OS:            posix Darwin 10.3.2 Darwin Kernel Version 10.3.2: Wed Mar
17 14:55:00 PDT 2010; root:xnu-1504.5.30~3/RELEASE_I386
 Distribution:   10.6.3/i386
 Present:       cPickle, ctypes, gzip, numpy
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good
scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, hcluster,
lars, libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp ge
2.4, nifti, nifti ge 0.20090205.1, nose, openopt, pylab, pylab plottable,
pywt, pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy,
running ipython env, scipy, sg ge 0.6.4, sg_fixedcachesize, shogun,
shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svrlight, weave
 Versions of critical externals:
  ctypes      : 1.1.0
  numpy       : 1.5.0
 PyMVPA Environment Variables:
 PyMVPA Runtime Configuration:
  have griddata = no
  have good scipy.stats.rdist = no
  have pylab plottable = no
  have pywt wp reconstruct = no
  have mdp = no
  have lxml = no
  have running ipython env = no
  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 = no
  have shogun.krr = no
  have nifti ge 0.20090205.1 = no
  have nose = no
  have weave = no
  have atlas_fsl = no
  have ctypes = yes
  have hcluster = no
  have sg ge 0.6.4 = no
  have good scipy.stats.rv_discrete.ppf = no
  have libsvm verbosity control = no
  have mdp ge 2.4 = no
  have shogun.svrlight = no
  have rpy = no
  have shogun = no
  have glmnet = no
  have lars = no
  have nifti = no
  have atlas_pymvpa = no
  have cpickle = yes
  have numpy = yes
  have pylab = no
  have shogun.lightsvm = no
  have pywt = no
  have gzip = yes

  verbose = 1

> just to make sure, something like
> python -c 'import nifti'
> works without any smoke?  what is also the output of
> python -c 'import mvpa; print mvpa.wtf()'
> ?
> P.S. Common problem on OSX is the hell of mixes of different pythons and
> corresponding modules installed via variety of methods (local, macports,
> etc) since there is no uniform one "out of the box" installation
> mechanism, i.e. like on Debian ;-)  thus for the best experience we just
> advice users to use http://neuro.debian.net/vm.html.
> On Thu, 28 Oct 2010, tbeck at artsci.wustl.edu wrote:
>> I've installed pymvpa on Mac OSX 10.6.3.  The installation went fine
>> initially, but when I try to import NiftiDataset I get the error:
>> RuntimeError: Required external 'nifti' was not found
>> I've installed pynifti through macports per the instructions, and I can
>> see the py26-pynifti directory where it's been created.  I've copied
>> that
>> directory over to the directory where mvpa is installed just in case but
>> no cigar.
>> has anyone reported a similar problem with PyNifti before?
> --
>                                   .-.
> =------------------------------   /v\  ----------------------------=
> Keep in touch                    // \\     (yoh@|www.)onerussian.com
> Yaroslav Halchenko              /(   )\               ICQ#: 60653192
>                    Linux User    ^^-^^    [175555]
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