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 <[email protected]>: > 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: [email protected] 11:28:34 $ git remote -v origin git://github.com/hanke/PyMVPA.git (fetch) origin git://github.com/hanke/PyMVPA.git (push) [email protected] 11:28:38 $ git log -1 commit 777ef3da166872fe6c4e24a4a3933ae20c90e689 Merge: e933165 7e34d24 Author: Michael Hanke <[email protected]> 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. ;) [email protected] 11:03:14 $ python setup.py build [email protected] 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 _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
