[pymvpa] building with setup.py

Tue Feb 9 19:37:28 UTC 2010

Hey Yarik,

Sorry this took so long.  I pulled the latest version from Micheal's
github repos, just realizing now that you asked me to test the 0.4
branch, hope this test is still informative.  If not, let me know.  In
summary, the build and install worked as I expected, on both my OSX
laptop and my FC12 desktop with system libsvm.  The output from OSX is
below, I'll send the 'system libsvm' output in another email.

Chris

2010/2/3 Yaroslav Halchenko <lists at onerussian.com>:
> Hi Chris,
>
> I wonder if you could help me out with testing either building works
> fine now and you get libsvm etc available "by default"... it is maint/0.4 branch
> from alioth or github repos of pymvpa.
>
> Also, if you have system wide installed libsvm it would be great if you
> tested it with
>
> --with-system-libsvm
>
> switch.

#### Which version and from where:

cburns at pymvpa.git 11:28:34 $ git remote -v
origin	git://github.com/hanke/PyMVPA.git (fetch)
origin	git://github.com/hanke/PyMVPA.git (push)

cburns at pymvpa.git 11:28:38 $ git log -1
commit 777ef3da166872fe6c4e24a4a3933ae20c90e689
Merge: e933165 7e34d24
Author: Michael Hanke <michael.hanke at gmail.com>
Date:   Tue Feb 9 10:48:41 2010 -0500

    Merge remote branch 'alioth/yoh/master' into mh/master

#### Standard build and install commands.  Did not include output to
reduce noise figuring "mvpa.wtf()" would be more informative.  ;)

cburns at pymvpa.git 11:03:14 $ python setup.py build

cburns at pymvpa.git 11:03:33 $ python setup.py install --prefix=$HOME/local

#### Importing, wtf() and tests
In [1]: import mvpa

In [2]: mvpa.__version__
Out[2]: '0.5.0.dev'

In [3]: from mvpa.clfs.svm import LinearNuSVMC

In [4]: mvpa.wtf()
Out[4]:
Current date:   2010-02-09 11:18
PyMVPA:
 Version:       0.5.0.dev
 Path:
/Users/cburns/local/lib/python2.5/site-packages/mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/Users/cburns/local/lib/python2.5/site-packages/mvpa/.. is not under
GIT"
SYSTEM:
 OS:            posix Darwin 9.8.0 Darwin Kernel Version 9.8.0: Wed
Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
 Distribution:   10.5.8/i386
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, libsvm, libsvm verbosity
control, matplotlib, nifti, nifti ge 0.20090205.1, nose, numpy, pylab,
pylab plottable, running ipython env, scipy, weave
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, h5py,
hcluster, lars, lxml, mdp, mdp ge 2.4, openopt, pprocess, pywt, pywt
wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy, rpy2, sg ge
0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr,
shogun.lightsvm, shogun.mpd, shogun.svrlight
 Versions of critical externals:
  ipython     : 0.10
  scipy       : 0.7.1
  numpy       : 1.3.0
  ctypes      : 1.0.3
  matplotlib  : 0.98.6svn
  nifti       : 0.20090303.1
  numpy       : 1.3.0
 Matplotlib backend: MacOSX
RUNTIME:
 PyMVPA Environment Variables:
  PYTHONPATH          :
".:/Users/cburns/src/utils:/Users/cburns/src/nitools:/Users/cburns/local/lib/python2.5/site-packages/:/usr/local/lib/python2.5/site-packages/:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5"
 PyMVPA Runtime Configuration:
  [externals]
  have griddata = yes
  have pprocess = no
  have good scipy.stats.rdist = yes
  have pylab plottable = yes
  have pywt wp reconstruct = no
  have h5py = no
  have lxml = no
  have running ipython env = yes
  have sg_fixedcachesize = no
  have elasticnet = no
  have shogun.mpd = no
  have matplotlib = yes
  have pywt wp reconstruct fixed = no
  have scipy = yes
  have reportlab = no
  have openopt = no
  have libsvm = yes
  have shogun.krr = no
  have nifti ge 0.20090205.1 = yes
  have nose = yes
  have weave = yes
  have atlas_fsl = no
  have ctypes = yes
  have hcluster = no
  have sg ge 0.6.4 = no
  have sg ge 0.6.5 = no
  have good scipy.stats.rv_discrete.ppf = yes
  have libsvm verbosity control = yes
  have mdp ge 2.4 = no
  have shogun.svrlight = no
  have rpy = no
  have lars = no
  have glmnet = no
  have shogun = no
  have nifti = yes
  have atlas_pymvpa = no
  have cpickle = yes
  have mdp = no
  have numpy = yes
  have pylab = yes
  have rpy2 = no
  have shogun.lightsvm = no
  have pywt = no
  have gzip = yes

  [general]
  verbose = 1

In [5]: mvpa.test()
WARNING: Testing for availability of external software packages. Test
cases depending on missing packages will not be part of the test
suite.
 * Please note: warnings are printed only once, but underlying problem
might occur many times *
WARNING: pprocess is not available.
WARNING: reportlab is not available.
WARNING: rpy is not available.
WARNING: pywt is not available.
WARNING: mdp is not available.
WARNING: lars is not available.
WARNING: lxml is not available.
WARNING: h5py is not available.
WARNING: shogun.krr is not available.
WARNING: shogun.svrlight is not available.
WARNING: elasticnet is not available.
WARNING: shogun.mpd is not available.
WARNING: atlas_pymvpa is not available.
WARNING: shogun is not available.
WARNING: sg ge 0.6.4 is not available.
WARNING: mdp ge 2.4 is not available.
WARNING: hcluster is not available.
WARNING: rpy2 is not available.
WARNING: sg ge 0.6.5 is not available.
WARNING: atlas_fsl is not available.
WARNING: glmnet is not available.
WARNING: openopt is not available.
WARNING: shogun.lightsvm is not available.
WARNING: sg_fixedcachesize is not available.
WARNING: pywt wp reconstruct fixed is not available.
WARNING: pywt wp reconstruct is not available.
...................F.......................................................................................................................................F.......................
======================================================================
FAIL: Perform sweeping over provided keyword arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/cburns/local/lib/python2.5/site-packages/mvpa/tests/test_transerror.py",
line 183, in test_null_dist_prob
    % null_prob)
AssertionError:
 Single scenario lead to failures of unittest test_null_dist_prob:
  on
    l_clf=FeatureSelectionClassifier(clf=SVM(svm_impl='C_SVC',
kernel=LinearLSKernel(), probability=1), e ... :
     Failed to check that the result is highly significant (got
0.100000) since we know that the data has signal
    l_clf=FeatureSelectionClassifier(clf=SVM(svm_impl='C_SVC',
kernel=LinearLSKernel(), probability=1), e ... :
     Failed to check that the result is highly significant (got
0.100000) since we know that the data has signal

======================================================================
FAIL: Very basic testing -- just to see if it doesn't crash
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/cburns/local/lib/python2.5/site-packages/mvpa/tests/test_base.py",
line 24, in test_wtf
    self.failUnless(len(sinfo) > len(sinfo_excludes))
AssertionError

----------------------------------------------------------------------
Ran 179 tests in 144.526s

FAILED (failures=2)
MVPA_SEED=1998088232
...
----------------------------------------------------------------------
Ran 3 tests in 0.009s

OK
.......................
----------------------------------------------------------------------
Ran 23 tests in 0.205s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.004s

OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.004s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.010s

OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.027s

OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.018s

OK
.....
----------------------------------------------------------------------
Ran 5 tests in 0.111s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.039s

OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.433s

OK
.
----------------------------------------------------------------------
Ran 1 test in 0.069s

OK
.......
----------------------------------------------------------------------
Ran 7 tests in 24.866s

OK