[pymvpa] SMLR shared library not found

Wed Mar 23 22:48:33 UTC 2011

To Thorsten and Michael thanks for reply but i thought i needed to manually install swig to help me install libsvm as the error still persists below when i do from mvpa.suite import*.  I have installed latest version by using snapshot command when i run it everything is up to date it says, even though it still says pymvpa-0.6.0~rc1 from mvpa.wtf and i don't have libsvm built or installed which i need, so i tried to do it manually. I still have no success though.

Any help would be great.
thanks
Amit

from mvpa.suite import *
WARNING: Failed to load fast implementation of SMLR.  May be you forgotten to build it.  We will use much slower pure-Python version. Original exception was /home/amit/pymvpa-0.6.0~rc1/mvpa/clfs/libsmlrc/smlrc.pyd: cannot open shared object file: No such file or directory
 * Please note: warnings are printed only once, but underlying problem might occur many times *
WARNING: SMLR: C implementation is not available. Using pure Python one
/usr/lib/pymodules/python2.6/matplotlib/numerix/__init__.py:18: DeprecationWarning: 
**********************************************************
matplotlib.numerix and all its subpackages are deprecated.
They will be removed soon.  Please use numpy instead.
**********************************************************

Current date:   2011-03-23 22:07
PyMVPA:
 Version:       0.6.0~rc1
 Hash:          feda3f526efd71a5ae34f0c1fd3d8f2334d5f412
 Path:          mvpa/__init__.py
 Version control (GIT):
 GIT information could not be obtained due "mvpa/.. is not under GIT"
SYSTEM:
 OS:            posix Linux 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010
 Distribution:  Ubuntu/10.10/maverick
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, matplotlib, mdp, mdp ge 2.4, nibabel, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct, reportlab, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.mpd, shogun.svmocas
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, hcluster, lars, libsvm, libsvm verbosity control, lxml, mass, nipy, nose, openopt, pprocess, pywt wp reconstruct fixed, rpy2, running ipython env, shogun.lightsvm, shogun.svrlight, skl, weave
 Versions of critical externals:
  shogun:full : 0.9.3_r4889_2010-05-27_20:52_
  shogun:rev  : 4889
  reportlab   : 2.4
  shogun      : 0.9.3
  matplotlib  : 0.99.3
  scipy       : 0.7.2
  mdp         : 2.6
  numpy       : 1.3.0
  ctypes      : 1.1.0
  matplotlib  : 0.99.3
  nifti       : failed to query due to "nifti is not a known dependency key."
  numpy       : 1.3.0
  pywt        : 0.2.0
  shogun      : v0.9.3_r4889_2010-05-27_20:52_
 Matplotlib backend: TkAgg
RUNTIME:
 PyMVPA Environment Variables:
   PyMVPA Runtime Configuration:
  [externals]
  have griddata = yes
  have pprocess = no
  have good scipy.stats.rdist = yes
  have pylab plottable = yes
  have pywt wp reconstruct = yes
  have ctypes = yes
  have lxml = no
  have running ipython env = no
  have nibabel = yes
  have sg_fixedcachesize = yes
  have elasticnet = no
  have shogun.mpd = yes
  have matplotlib = yes
  have pywt wp reconstruct fixed = no
  have scipy = yes
  have reportlab = yes
  have openopt = no
  have libsvm = no
  have nose = no
  have weave = no
  have atlas_fsl = no
  have h5py = yes
  have hcluster = no
  have sg ge 0.6.4 = yes
  have sg ge 0.6.5 = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have skl = no
  have mdp ge 2.4 = yes
  have shogun.svrlight = no
  have lars = no
  have shogun.svmocas = yes
  have nipy = no
  have glmnet = no
  have mass = no
  have shogun = yes
  have libsvm verbosity control = no
  have atlas_pymvpa = no
  have shogun.krr = yes
  have cpickle = yes
  have mdp = yes
  have numpy = yes
  have pylab = yes
  have rpy2 = no
  have shogun.lightsvm = no
  have pywt = yes
  have gzip = yes

> Date: Wed, 23 Mar 2011 15:24:53 +0100
> From: thorstenkranz at googlemail.com
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Subject: Re: [pymvpa] SMLR shared library not found
> 
> I'm not sure why the installation from NeuroDebian doesn't work for
> you, but maybe you have some old rests of previous installs on your
> box.
> 
> Why would you want to install swig manuall? Just do
> 
> sudo apt-get install swig
> 
> or similar in a terminal, this should get you swig. It must be
> callable in a terminal in order to let the installation complete.
> 
> Greetings,
> Thorsten
> 
> 2011/3/23 amit patel <damitamit82 at hotmail.co.uk>:
> > Hello
> >
> > I have installed the new updates using apt-get install python-mvpa-snapshot
> > from your
> >> NeuroDebian repository but error still persists?
> >
> > so doing it manually(following instructions) i did this
> >
> > amit at amit-MS-7346:~/pymvpa-0.6.0~rc1$ python setup.py install --with-libsvm
> >
> > i get this error
> > error: command 'swig' failed with exit status 1
> > So i presume i have to tell it where i downloaded swig? it is in
> > /home/amit/swig-2.0.2
> >
> > so do i do this python setup.py install --with-libsvm
> > [-I/home/amit/swig-2.0.2], only this does not work. Also don't i have to
> > tell it where libsvm-3.0 is as well?
> >
> > I am according to instructions have to do something like this
> >
> > python setup.py build_ext --with-libsvm \
> >     [ -I<LIBSVM_INCLUDEDIR> -L<LIBSVM_LIBDIR> ]
> >
> > any help would be great......... thank you
> >
> > Amit
> >
> >
> >
> >
> >> Date: Tue, 22 Mar 2011 15:59:50 -0400
> >> From: debian at onerussian.com
> >> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> >> Subject: Re: [pymvpa] SMLR shared library not found
> >>
> >> on ubuntu -- just apt-get install python-mvpa-snapshot from our
> >> NeuroDebian repository:
> >>
> >> http://neuro.debian.net
> >>
> >> otherwise follow
> >> http://www.pymvpa.org/installation.html#alternative-build-procedure
> >>
> >> On Tue, 22 Mar 2011, amit patel wrote:
> >> > No such file or directory
> >> > * Please note: warnings are printed only once, but underlying problem
> >> > might occur many times *
> >> > WARNING: SMLR: C implementation is not available. Using pure Python one
> >> --
> >> .-.
> >> =------------------------------ /v\ ----------------------------=
> >> Keep in touch // \\ (yoh@|www.)onerussian.com
> >> Yaroslav Halchenko /( )\ ICQ#: 60653192
> >> Linux User ^^-^^ [175555]
> >>
> >>
> >>
> >> _______________________________________________
> >> Pkg-ExpPsy-PyMVPA mailing list
> >> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
> >
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
> >
> >
> 
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