[pymvpa] reply-to

Wed Apr 22 18:57:13 UTC 2009

hey list,

during my correspondence last night re pymvpa installation, i was 
hitting reply, and inadvertently sending emails solely to scott (rather 
than to the whole list).

i don't want to tell you how to run your circus, but maybe setting 
thereply-to to the list might be a good plan, since that *is* the 
behavior that we want to foster. alternatively, i could just pay closer 
attention next time. or both :)

g

Scott Gorlin wrote:
> shoot, the api changed since that hack.
> 
> try instead:
> 
> from mvpa.base import cfg
> cfg.set('externals', 'have shogun', 'no')
> 
> from mvpa.suite import *
> 
> wrt those things like lapack, i'm not too clear on these things, but i 
> believe they are supposed to be optional dependencies which speed things 
> up.  i just installed all of them until everything in the shogun 
> installer said yes.
> 
> i think that RPy thing is a bug induced by you changing _KNOWN, I don't 
> think there's any reason you need R
> 
> ps please forward all responses to the mailing list, so others may glean 
> wisdom from our proceedings ;)
> 
> Greg Detre wrote:
>>  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'
>>
>>

-- 

---
Greg Detre
cell: 617 642 3902
email: greg at gregdetre.co.uk
web: http://www.princeton.edu/~gdetre/