Yarik, Here's the results of using the --with-system-libsvm switch: 2010/2/3 Yaroslav Halchenko <[email protected]>: > 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. [email protected] 11:17:17 $ python setup.py build --with-system-libsvm [email protected] 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: 96...@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]: _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
