[pymvpa] LinearCSVMC module not found

Thu Sep 24 17:56:32 UTC 2015

The .so files are found in site-packages/mvpa2/clfs file.
Strange thing is, even those files are in the mvpa2 module, when I called out mvpa2.wtf(), it shows that libsvm has not been loaded yet. I used ‘from mvpa2.suite import *’ to load the module.

There are two warnings when I loaded the module, and not sure if those could help:

/Users/tumo/anaconda/lib/python2.7/site-packages/numpy/lib/utils.py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead!
warnings.warn(depdoc, DeprecationWarning)
/Users/tumo/anaconda/lib/python2.7/site-packages/numpy/lib/utils.py:95: DeprecationWarning: `scipy.linalg.calc_lwork` is deprecated!

calc_lwork was an internal module in Scipy and has been removed.

Several functions in scipy.linalg.lapack have *_lwork variants
that perform the lwork calculation (from Scipy >= 0.15.0), or
allow passing in LWORK=-1 argument to perform the computation.

Here you are the wtf() output:

Current date: 2015-09-24 12:51
PyMVPA:
Version: 2.4.0
Hash: $Format:%H$
Path: /Users/tumo/anaconda/lib/python2.7/site-packages/mvpa2/__init__.pyc
Version control (GIT):
GIT information could not be obtained due "/Users/tumo/anaconda/lib/python2.7/site-packages/mvpa2/.. is not under GIT"
SYSTEM:
OS: posix Darwin 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64
Distribution: 10.10.5/x86_64
EXTERNALS:
Present: cPickle, ctypes, good scipy.stats.rv_continuous._reduce_func(floc,fscale), good scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, hdf5, ipython, libsvm verbosity control, lxml, matplotlib, mock, nose, numpy, numpy_correct_unique, pylab, pylab plottable, running ipython env, scipy, skl, statsmodels, weave
Absent: atlas_fsl, atlas_pymvpa, cran-energy, elasticnet, glmnet, good scipy.stats.rdist, hcluster, joblib, lars, liblapack.so, libsvm, mass, mdp, mdp ge 2.4, nibabel, nipy, nipy.neurospin, numpydoc, openopt, pprocess, pywt, pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy2, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight
Versions of critical externals:
ctypes : 1.1.0
h5py : 2.5.0
hdf5 : 1.8.15
ipython : 3.2.0
lxml : 3.4.4
matplotlib : 1.4.3
mock : 1.0.1
numpy : 1.9.2
scipy : 0.15.1
skl : 0.16.1
Matplotlib backend: MacOSX
RUNTIME:
PyMVPA Environment Variables:
PYTHONEXECUTABLE : "/Users/tumo/anaconda/bin/python"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = yes
have ipython = yes
have numpy = yes
have scipy = yes
have matplotlib = yes
have h5py = yes
have reportlab = no
have weave = yes
have good scipy.stats.rdist = no
have good scipy.stats.rv_discrete.ppf = yes
have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes
have pylab = yes
have lars = no
have elasticnet = no
have glmnet = no
have skl = yes
have ctypes = yes
have libsvm = no
have shogun = no
have openopt = no
have nibabel = no
have mdp = no
have mdp ge 2.4 = no
have nipy = no
have statsmodels = yes
have pywt = no
have cpickle = yes
have gzip = yes
have cran-energy = no
have griddata = yes
have nipy.neurospin = no
have lxml = yes
have atlas_fsl = no
have atlas_pymvpa = no
have hcluster = no
have hdf5 = yes
have joblib = no
have liblapack.so = no
have libsvm verbosity control = yes
have mass = no
have mock = yes
have nose = yes
have numpy_correct_unique = yes
have numpydoc = no
have pprocess = no
have pylab plottable = yes
have pywt wp reconstruct = no
have pywt wp reconstruct fixed = no
have rpy2 = no
have sg ge 0.6.4 = no
have sg ge 0.6.5 = no
have sg_fixedcachesize = no
have shogun.krr = no
have shogun.lightsvm = no
have shogun.mpd = no
have shogun.svmocas = no
have shogun.svrlight = no

On 9/24/15, 5:57 AM, "Pkg-ExpPsy-PyMVPA on behalf of Nick Oosterhof" <pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu.edu at lists.alioth.debian.org<mailto:pkg-exppsy-pymvpa-bounces+guangsheng.liang=ttu.edu at lists.alioth.debian.org> on behalf of n.n.oosterhof at googlemail.com<mailto:n.n.oosterhof at googlemail.com>> wrote:

On 24 Sep 2015, at 11:45, Liang, Guangsheng <guangsheng.liang at ttu.edu<mailto:guangsheng.liang at ttu.edu>> wrote:
Yes, I do find smlrc.so, and _svmc.so file after installing anaconda on my computer.

Are these in the ${PYMVPA_ROOT}/mvpa2 directory, or in a ${PYMVPA_ROOT}//build/*/mvpa2 directory? In the latter case, you may have to copy them to the ${PYMVPA_ROOT}/mvpa2 directory.
In more detail, as described earlier [1], I noticed that when running python setup.py build_ext on OSX, the output is stored in the build directory. Manually copying the files to the mvpa2 directory made them accessible in PyMVPA. Specifically, the following worked when run from the PyMVPA root directory:

    for ext in .so .o; do for i in `find build -iname "*${ext}"`; do j=`echo $i | cut -f3- -d/`; cp $i $j; done; done

Can you try and see if that resolves the issue? If it does not, can you provide the full error message and also, from within python/ipython, the output of:

    import mvpa2
    mvpa2.wtf()

[1] http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q3/003176.html

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