Thank you Gaël, I can now install and import.
The tests are failing though, log attached.
thanks,
bryan
On Fri, May 11, 2012 at 10:22 AM, Gael Varoquaux <
[email protected]> wrote:
> I could reproduce using an install rather than a build inplace, and I
> pushed a fix.
>
> Thanks for reporting and sorry for the bug,
>
> Gaël
>
> On Fri, May 11, 2012 at 10:13:51AM -0700, W. Bryan Smith wrote:
> > On Fri, May 11, 2012 at 3:03 PM, W. Bryan Smith <[email protected]>
> wrote:
>
> > >> the source was pulled from git about 20 minutes before i sent the
> email.
>
>
> > > I haven't tried to actually run "python setup.py install" so there may
> > > remain problems. But, have you tried to run "make clean" or "python
> > > setup.py clean" before installing?
>
>
>
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Running unit tests and doctests for sklearn
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/util.py:14:
DeprecationWarning: The compiler package is deprecated and removed in Python
3.x.
from compiler.consts import CO_GENERATOR
NumPy version 1.5.1
NumPy is installed in
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy
Python version 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) [GCC 4.2.1 (Based on
Apple Inc. build 5658) (LLVM build 2335.15.00)]
nose version 1.1.2
.................S.............................../Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/cluster/spectral.py:77:
UserWarning: pyamg not available, using scipy.sparse
warnings.warn('pyamg not available, using scipy.sparse')
.S.....................EE..SS.S................................../Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/dict_learning.py:501:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
init=code, n_jobs=n_jobs)
../Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/dict_learning.py:745:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
alpha=self.transform_alpha, n_jobs=self.n_jobs)
.../Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/dict_learning.py:667:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
alpha=alpha).T
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/dict_learning.py:697:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
n_jobs=n_jobs)
....S/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/tests/test_dict_learning.py:124:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
code = sparse_encode(X, V, algorithm=algo)
./Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/tests/test_dict_learning.py:132:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
code = sparse_encode(X, V, alpha=0.001)
............................................../Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/parallel.py:87:
UserWarning: Please note: the interface of sparse_encode has changed: It now
follows the dictionary learning API and it also handles parallelization. Please
read the docstring for more information.
return self.func(*args, **kwargs)
.....SEE................................................/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/test/test_func_inspect.py:122:
UserWarning: Cannot inspect object <functools.partial object at 0x109a4edb8>,
ignore list will not work.
nose.tools.assert_equal(filter_args(ff, ['y'], (1, )),
.........................................................................................________________________________________________________________________________
test_memory setup
________________________________________________________________________________
________________________________________________________________________________
test_memory teardown
________________________________________________________________________________
..________________________________________________________________________________
test_memory setup
________________________________________________________________________________
..........................................................................................................................________________________________________________________________________________
test_memory teardown
________________________________________________________________________________
.________________________________________________________________________________
setup numpy_pickle
________________________________________________________________________________
.....................................Exception AttributeError:
AttributeError("'NoneType' object has no attribute 'tell'",) in <bound method
memmap.__del__ of memmap(2.315841784746324e+77)> ignored
Exception AttributeError: AttributeError("'NoneType' object has no attribute
'tell'",) in <bound method memmap.__del__ of memmap(2.315841784746324e+77)>
ignored
Exception AttributeError: AttributeError("'NoneType' object has no attribute
'tell'",) in <bound method memmap.__del__ of memmap(2.315841784746324e+77)>
ignored
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/test/test_numpy_pickle.py:182:
Warning: file
"/var/folders/vh/m7v3sj2d0md3c1v53l12hnk80000gn/T/tmpP7reiy/test.pkl492"
appears to be a zip, ignoring mmap_mode "r" flag passed
numpy_pickle.load(this_filename, mmap_mode='r')
Exception AttributeError: AttributeError("'NoneType' object has no attribute
'tell'",) in <bound method memmap.__del__ of memmap(2.315841784746324e+77)>
ignored
.....________________________________________________________________________________
teardown numpy_pickle
________________________________________________________________________________
............An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (39, 0))
..........................................................................................EE.............S....................................................................................................................................................................................................................................................................................FEFEFE.........................................................E..........................EEE.........................................................................................................SSS....S....S.......................................................................................EE
======================================================================
ERROR: Doctest: sklearn.datasets.base.load_sample_image
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: Doctest: sklearn.datasets.base.load_sample_images
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: Doctest: sklearn.ensemble.gradient_boosting.GradientBoostingClassifier
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: Doctest: sklearn.ensemble.gradient_boosting.GradientBoostingRegressor
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: Doctest: sklearn.linear_model.randomized_l1.RandomizedLasso
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: Doctest: sklearn.linear_model.randomized_l1.RandomizedLogisticRegression
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.py",
line 395, in tearDown
delattr(builtin_mod, self._result_var)
AttributeError: _
======================================================================
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (47, 0))
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/Users/bryan/<ipython-input-2-2608184d6e44> in <module>()
----> 1 sklearn.test()
/Library/Python/2.7/site-packages/scikit_learn-0.12_git-py2.7-macosx-10.7-intel.egg/sklearn/__init__.pyc
in test(self, label, verbose, extra_argv, doctests, coverage)
38 return super(_NoseTester, self).test(label=label,
verbose=verbose,
39 extra_argv=extra_argv,
---> 40 doctests=doctests,
coverage=coverage)
41
42 try:
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/testing/nosetester.pyc
in test(self, label, verbose, extra_argv, doctests, coverage)
325 doctests, coverage)
326 from noseclasses import NumpyTestProgram
--> 327 t = NumpyTestProgram(argv=argv, exit=False, plugins=plugins)
328 return t.result
329
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/core.pyc in
__init__(self, module, defaultTest, argv, testRunner, testLoader, env, config,
suite, exit, plugins, addplugins)
116 self, module=module, defaultTest=defaultTest,
117 argv=argv, testRunner=testRunner, testLoader=testLoader,
--> 118 **extra_args)
119
120 def makeConfig(self, env, plugins=None):
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/main.pyc
in __init__(self, module, defaultTest, argv, testRunner, testLoader, exit,
verbosity, failfast, catchbreak, buffer)
93 self.progName = os.path.basename(argv[0])
94 self.parseArgs(argv)
---> 95 self.runTests()
96
97 def usageExit(self, msg=None):
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/testing/noseclasses.py
in runTests(self)
347 self.testRunner = plug_runner
348
--> 349 self.result = self.testRunner.run(self.test)
350 self.success = self.result.wasSuccessful()
351 return self.success
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/core.pyc in
run(self, test)
61 test(result)
62 stop = time.time()
---> 63 result.printErrors()
64 result.printSummary(start, stop)
65 self.config.plugins.finalize(result)
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/result.pyc in
printErrors(self)
101 """Overrides to print all errorClasses errors as well.
102 """
--> 103 _TextTestResult.printErrors(self)
104 for cls in self.errorClasses.keys():
105 storage, label, isfail = self.errorClasses[cls]
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/runner.pyc
in printErrors(self)
106 if self.dots or self.showAll:
107 self.stream.writeln()
--> 108 self.printErrorList('ERROR', self.errors)
109 self.printErrorList('FAIL', self.failures)
110
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/runner.pyc
in printErrorList(self, flavour, errors)
112 for test, err in errors:
113 self.stream.writeln(self.separator1)
--> 114 self.stream.writeln("%s: %s" %
(flavour,self.getDescription(test)))
115 self.stream.writeln(self.separator2)
116 self.stream.writeln("%s" % err)
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/result.pyc in
getDescription(self, test)
80 def getDescription(self, test):
81 if self.descriptions:
---> 82 return test.shortDescription() or str(test)
83 else:
84 return str(test)
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.pyc in
__str__(self)
49 if name is not None:
50 return name
---> 51 return str(self.test)
52
53 def __repr__(self):
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.pyc
in __repr__(self)
369
370 def __repr__(self):
--> 371 name = self.id()
372 name = name.split('.')
373 return "%s (%s)" % (name[-1], '.'.join(name[:-1]))
/Library/Python/2.7/site-packages/nose-1.1.2-py2.7.egg/nose/plugins/doctests.pyc
in id(self)
364 if filename is not None:
365 pk = getpackage(filename)
--> 366 if not name.startswith(pk):
367 name = "%s.%s" % (pk, name)
368 return name
TypeError: expected a character buffer object------------------------------------------------------------------------------
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will include endpoint security, mobile security and the latest in malware
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