On 04/05/2012 12:46 PM, Emanuele Olivetti wrote:
Hi,
this morning I attempted the first command of the PyMVPA tutorial
on an updated NeuroDebian virtual machine and observed this:
-------
brain@neurodebian:~$ python
Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48)
[GCC 4.4.5] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from mvpa2.tutorial_suite import *
/usr/lib/pymodules/python2.6/scikits/learn/__init__.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
/usr/lib/pymodules/python2.6/sklearn/hmm.py:24: UserWarning: sklearn.hmm is orphaned,
undocumented and has known numerical stability issues. If nobody volunteers to write
documentation and make it more stable, this module will be removed in version 0.11.
warnings.warn('sklearn.hmm is orphaned, undocumented and has known numerical'
/usr/lib/pymodules/python2.6/scikits/learn/lda.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
/usr/lib/pymodules/python2.6/scikits/learn/grid_search.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
/usr/lib/pymodules/python2.6/scikits/learn/naive_bayes.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
/usr/lib/pymodules/python2.6/scikits/learn/neighbors.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
/usr/lib/pymodules/python2.6/scikits/learn/qda.py:2: UserWarning: scikits.learn
namespace is deprecated, please use sklearn instead
warnings.warn('scikits.learn namespace is deprecated, please use sklearn
instead')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/pymodules/python2.6/mvpa2/tutorial_suite.py", line 15, in
<module>
from mvpa2.suite import *
File "/usr/lib/pymodules/python2.6/mvpa2/suite.py", line 154, in <module>
if externals.exists('mdp ge 2.4'):
File "/usr/lib/pymodules/python2.6/mvpa2/base/externals.py", line 595, in
exists
exec _KNOWN[dep]
File "<string>", line 1, in <module>
File "/usr/lib/pymodules/python2.6/mdp/__init__.py", line 166, in <module>
import nodes
File "/usr/lib/pymodules/python2.6/mdp/nodes/__init__.py", line 54, in
<module>
del convolution_nodes
NameError: name 'convolution_nodes' is not defined
>>>
-----
As far as I understand, besides the warning on the scikits->sklearn renaming,
there is
an issue with MDP. I am digging it but in case you already know that I am
sending this message immediately.
After a little digging I found out that the package python-mdp has some other
bigger issues: even "import mdp" fails. This is quite unexpected...
This tiny change in MDP seems to solve the issue of my previous message though.
-------------------------------------------
--- __init__.py.original 2012-04-05 07:46:13.000000000 -0400
+++ __init__.py 2012-04-05 07:48:40.000000000 -0400
@@ -51,17 +51,17 @@
if numx_description == 'scipy':
from convolution_nodes import Convolution2DNode
__all__ += ['Convolution2DNode']
- del convolution_nodes
+ # del convolution_nodes
if config.has_shogun:
from shogun_svm_classifier import ShogunSVMClassifier
__all__ += ['ShogunSVMClassifier']
- del shogun_svm_classifier
+ # del shogun_svm_classifier
if config.has_libsvm:
from libsvm_classifier import LibSVMClassifier
__all__ += ['LibSVMClassifier']
- del libsvm_classifier
+ # del libsvm_classifier
if config.has_scikits:
import scikits_nodes
--------------------------------------------
Best,
Emanuele
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