hey scott,
thanks for your help.
> i wonder if shogun is installed correctly. looking closer at your
> error, looks like it's looking for a lapack library. have you
> installed lapack and all those goodies?
i haven't explicitly installed LAPACK or anything like that. i figured
those dependencies would have been taken care of by the package
manager...
it looks like i have:
libblas3gf
libblas-dev
liblapack3gf
but i don't have:
libatlas3gf-base
libatlas-base-dev
liblapack-dev
lapack3 (seems to be dud)
scalapack-*
> if you need shogun, i'd highly recommend installing the version from
> shogun-toolbox.org, which is many versions newer than ubuntu's.
> that should also take care of any dependencies it requires like
> lapack.
>
> do the libsvm backend classifiers work? if not then it may be that
> your libsvm installation didn't take for some reason, which is why
> it's trying to import from shogun (can't recall off the top of my
> head whether mvpa.suite will import the shogun libraries if libsvm
> isn't installed).
i'm new to this and don't know how to test those classifiers. just to
reiterate, it fails when i run:
from mvpa.suite import *
i can perhaps try those libsvm classifiers with per tomorrow if it's
going to be really diagnostic.
> there's also a workaround to prevent loading shogun even if it's
> installed. you shouldn't have needed this unless you actually had it
> installed previously, so I'm a bit confused why you're getting this
> error. however, prior to importing suite, try this:
>
> import mvpa.base.externals mvpa.base.externals._VERIFIED['shogun'] =
> False
>
> from mvpa.suite import *
you mentioned mvpa.base.externals._VERIFIED, but i don't seem to have
that. so instead, i tried _KNOWN. i don't know if that's what you had
meant. see the error below.
g
p.s. i'm only borrowing the machine from someone else, so i'd prefer
not to install RPy on it, since aptitude seems to want to upgrade all
kinds of other packages in order to do so. however, i can probably
install RPy tomorrow if that's necessary.
In [3]: mvpa.base.externals._KNOWN
Out[3]:
{'atlas_fsl': "__check_atlas_family('fsl')",
'atlas_pymvpa': "__check_atlas_family('pymvpa')",
'cPickle': 'import cPickle as __',
'ctypes': 'import ctypes as __',
'good scipy.stats.rdist': '__check_stablerdist()',
'griddata': 'import griddata as __',
'gzip': 'import gzip as __',
'hcluster': 'import hcluster as __',
'lars': "import rpy; rpy.r.library('lars')",
'libsvm': 'import mvpa.clfs.libsvmc._svm as __; x=__.convert2SVMNode',
'libsvm verbosity control': '__check_libsvm_verbosity_control();',
'lxml': 'from lxml import objectify as __',
'matplotlib': '__check_matplotlib()',
'mdp': 'import mdp as __',
'nifti': 'from nifti import NiftiImage as __',
'nifti >= 0.20090205.1': 'from nifti.clib import detachDataFromImage as
__',
'openopt': 'import scikits.openopt as __',
'pylab': '__check_pylab()',
'pylab plottable': '__check_pylab_plottable()',
'pywt': 'import pywt as __',
'pywt wp reconstruct': "__check_pywt(['wp reconstruct'])",
'pywt wp reconstruct fixed': "__check_pywt(['wp reconstruct fixed'])",
'rpy': 'import rpy as __',
'running ipython env': '__check_in_ipython()',
'scipy': 'import scipy as __',
'sg >= 0.6.4': '__check_shogun(3318)',
'sg_fixedcachesize': '__check_shogun(3043, [2456])',
'shogun': 'import shogun as __',
'shogun.lightsvm': 'import shogun.Classifier as __; x=__.SVMLight',
'shogun.mpd': 'import shogun.Classifier as __; x=__.MPDSVM',
'shogun.svrlight': 'from shogun.Regression import SVRLight as __',
'weave': '__check_weave()'}
In [4]: mvpa.base.externals._KNOWN['shogun'] = False
In [5]: from mvpa.suite import *
---------------------------------------------------------------------------
AttributeError Traceback (most recent call
last)
/qbert/home/greg/<ipython console> in <module>()
/var/lib/python-support/python2.5/mvpa/suite.py in <module>()
43 from mvpa.clfs.stats import *
44 if externals.exists('libsvm') or externals.exists('shogun'):
---> 45 from mvpa.clfs.svm import *
46 from mvpa.clfs.transerror import *
47 from mvpa.clfs.warehouse import *
/var/lib/python-support/python2.5/mvpa/clfs/svm.py in <module>()
51 debug('SVM', 'Default SVM backend is %s' % default_backend)
52
---> 53 if externals.exists('shogun'):
54 from mvpa.clfs import sg
55 SVM = sg.SVM
/var/lib/python-support/python2.5/mvpa/base/externals.pyc in exists(dep,
force, raiseException, issueWarning)
283 # importing RPy also involved starting a full-blown R
session, which can
284 # take seconds and therefore is quite nasty...
--> 285 if dep.count('rpy') or _KNOWN[dep].count('rpy'):
286 try:
287 from rpy import RException
AttributeError: 'bool' object has no attribute 'count'
