[pymvpa] setup.py build --with-system-libsvm

Tue Feb 9 19:43:47 UTC 2010

Yarik,  Here's the results of using the --with-system-libsvm switch:

2010/2/3 Yaroslav Halchenko <lists at onerussian.com>:
> I wonder if you could help me out with testing either building works
>
> Also, if you have system wide installed libsvm it would be great if you
> tested it with
>
> --with-system-libsvm

####  build and install commands.
cburns at pymvpa.git 11:17:17 $ python setup.py build --with-system-libsvm

cburns at pymvpa.git 11:17:26 $ python setup.py install --prefix=$HOME/local

#### Importing, wtf() and tests

In [1]: import mvpa
/home/cburns/local/lib64/python2.6/site-packages/mvpa/base/verbosity.py:19:
DeprecationWarning: the sets module is deprecated
  from sets import Set

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

In [3]: mvpa.wtf()
Out[3]:
Current date:   2010-02-09 11:17
PyMVPA:
 Version:       0.5.0.dev
 Path:
/home/cburns/local/lib64/python2.6/site-packages/mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due
"/home/cburns/local/lib64/python2.6/site-packages/mvpa/.. is not under
GIT"
SYSTEM:
 OS:            posix Linux 2.6.30.9-99.fc11.x86_64 #1 SMP Tue Nov 17
21:30:38 EST 2009
 Distribution:  fedora/11/Leonidas
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rv_discrete.ppf,
griddata, gzip, libsvm, libsvm verbosity control, matplotlib, nifti,
nifti ge 0.20090205.1, nose, numpy, pylab, pylab plottable, reportlab,
running ipython env, scipy
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good
scipy.stats.rdist, h5py, hcluster, lars, lxml, mdp, mdp ge 2.4,
openopt, pprocess, pywt, pywt wp reconstruct, pywt wp reconstruct
fixed, rpy, rpy2, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun,
shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svrlight, weave
 Versions of critical externals:
  ipython     : 0.10
  reportlab   : 2.3
  scipy       : 0.7.0
  numpy       : 1.3.0
  ctypes      : 1.1.0
  matplotlib  : 1.0.svn
  nifti       : 0.20090303.1
  numpy       : 1.3.0
 Matplotlib backend: GTKAgg
RUNTIME:
 PyMVPA Environment Variables:
  PYTHONPATH          :
".:/home/cburns/local/lib64/python2.6/site-packages/:/home/cburns/local/lib/python2.6/site-packages/:/usr/local/lib64/python2.6/site-packages/:/usr/local/lib/python2.6/site-packages/:/home/cburns/python2.6/Tools/scripts/:/home/cburns/src/epydoc-trunk/src/"
 PyMVPA Runtime Configuration:
  [externals]
  have griddata = yes
  have pprocess = no
  have good scipy.stats.rdist = no
  have pylab plottable = yes
  have pywt wp reconstruct = no
  have mdp = 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 = yes
  have openopt = no
  have libsvm = yes
  have h5py = no
  have shogun.krr = no
  have nifti ge 0.20090205.1 = yes
  have nose = yes
  have weave = no
  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 shogun = no
  have glmnet = no
  have lars = no
  have nifti = yes
  have atlas_pymvpa = no
  have cpickle = yes
  have numpy = yes
  have pylab = yes
  have rpy2 = no
  have shogun.lightsvm = no
  have pywt = no
  have gzip = yes

  [general]
  verbose = 1
 Process Information:
  Name:	ipython
  State:	R (running)
  Tgid:	24902
  Pid:	24902
  PPid:	24850
  TracerPid:	0
  Uid:	502	502	502	502
  Gid:	502	502	502	502
  Utrace:	0
  FDSize:	256
  Groups:	502
  VmPeak:	  530704 kB
  VmSize:	  530704 kB
  VmLck:	       0 kB
  VmHWM:	   61064 kB
  VmRSS:	   61060 kB
  VmData:	   44816 kB
  VmStk:	     248 kB
  VmExe:	       4 kB
  VmLib:	   51392 kB
  VmPTE:	    1092 kB
  Threads:	1
  SigQ:	4/43008
  SigPnd:	0000000000000000
  ShdPnd:	0000000000000000
  SigBlk:	0000000000000000
  SigIgn:	0000000001001004
  SigCgt:	0000000180000002
  CapInh:	0000000000000000
  CapPrm:	0000000000000000
  CapEff:	0000000000000000
  CapBnd:	ffffffffffffffff
  Cpus_allowed:	f
  Cpus_allowed_list:	0-3
  Mems_allowed:	00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
  Mems_allowed_list:	0
  voluntary_ctxt_switches:	245
  nonvoluntary_ctxt_switches:	195

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: rpy is not available.
WARNING: pywt is not available.
WARNING: shogun.krr is not available.
WARNING: atlas_pymvpa is not available.
WARNING: good scipy.stats.rdist is not available.
WARNING: mdp ge 2.4 is not available.
WARNING: hcluster is not available.
WARNING: pprocess is not available.
WARNING: shogun.lightsvm is not available.
WARNING: h5py is not available.
WARNING: pywt wp reconstruct is not available.
WARNING: mdp is not available.
WARNING: lars is not available.
WARNING: lxml is not available.
WARNING: shogun.svrlight is not available.
WARNING: elasticnet is not available.
WARNING: shogun.mpd is not available.
WARNING: shogun is not available.
WARNING: sg ge 0.6.4 is not available.
WARNING: pywt wp reconstruct fixed is not available.
WARNING: sg ge 0.6.5 is not available.
WARNING: rpy2 is not available.
WARNING: atlas_fsl is not available.
WARNING: weave is not available.
WARNING: glmnet is not available.
WARNING: openopt is not available.
WARNING: sg_fixedcachesize is not available.
...................F...................F...........................................................................................................................................
======================================================================
FAIL: Perform sweeping over provided keyword arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/cburns/local/lib64/python2.6/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

======================================================================
FAIL: Perform sweeping over provided keyword arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/cburns/local/lib64/python2.6/site-packages/mvpa/tests/test_clf.py",
line 171, in test_classifier_generalization
    % (cve, ds, len(ds.UT)))
AssertionError:
 Single scenario lead to failures of unittest test_classifier_generalization:
  on
    clf=FeatureSelectionClassifier(clf=kNN(k=2, dfx=<function
squared_euclidean_distance at 0x30a2cf8>, ... :
     Got transfer error 0.291667 on <Dataset: 96x14 at float64, <sa:
chunks,targets>, <fa: targets>, <a: bogus_features,nonbogus_features>>
with 4 labels

----------------------------------------------------------------------
Ran 179 tests in 58.495s

FAILED (failures=2)
...
----------------------------------------------------------------------
Ran 3 tests in 0.005s

OK
.......................
----------------------------------------------------------------------
Ran 23 tests in 0.086s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.002s

OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.002s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.006s

OK
....
----------------------------------------------------------------------
Ran 4 tests in 0.014s

OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.010s

OK
.....
----------------------------------------------------------------------
Ran 5 tests in 0.056s

OK
..
----------------------------------------------------------------------
Ran 2 tests in 0.009s

OK
...
----------------------------------------------------------------------
Ran 3 tests in 0.229s

OK
.
----------------------------------------------------------------------
Ran 1 test in 0.028s

OK
.......
----------------------------------------------------------------------
Ran 7 tests in 10.249s

OK
MVPA_SEED=2115110904

In [6]: