Hi Stanley. Thanks for letting us know. This particular test seems to be numerically unstable. I just adjusted this yesterday to work on my linux box, but the accuracy on your OS X seems to be even worse. We have to figure out how to test this more reliable. In the meantime, you shouldn't worry to much about this test failing.
This is locally linear embedding and works with the systems ARPACK as far as I know. Ensuring that this runs stable on a large number of different architectures is not so easy. Thanks for the report, it is appreciated and we will try to get rid of the error. Cheers, Andy ----- Ursprüngliche Mail ----- Von: "Stanley Wang" <[email protected]> An: [email protected] Gesendet: Sonntag, 5. August 2012 02:57:33 Betreff: [Scikit-learn-general] Error in "nosetests sklearn" output Hi, I have a failed test while running "nosetests sklearn": ............/Users/stanleynwang/Programming Projects/scikit-learn/sklearn/cluster/hierarchical.py:111: UserWarning: the number of connected components of the connectivity matrix is 2 > 1. Completing it to avoid stopping the tree early. % n_components) ..........................................S/Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/empirical_covariance_.py:60: UserWarning: Only one sample available. You may want to reshape your data array warnings.warn("Only one sample available. " \ ../Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/shrunk_covariance_.py:282: UserWarning: Only one sample available. You may want to reshape your data array warnings.warn("Only one sample available. " \ ./Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/shrunk_covariance_.py:439: UserWarning: Only one sample available. You may want to reshape your data array warnings.warn("Only one sample available. " \ ../Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/graph_lasso_.py:44: RuntimeWarning: invalid value encountered in absolute gap += alpha * (np.abs(precision_).sum() /Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/graph_lasso_.py:45: RuntimeWarning: invalid value encountered in absolute - np.abs(np.diag(precision_)).sum()) /Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/graph_lasso_.py:31: RuntimeWarning: invalid value encountered in absolute cost += alpha * (np.abs(precision_).sum() /Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/graph_lasso_.py:32: RuntimeWarning: invalid value encountered in absolute - np.abs(np.diag(precision_)).sum()) /Users/stanleynwang/Programming Projects/scikit-learn/sklearn/covariance/graph_lasso_.py:194: RuntimeWarning: invalid value encountered in absolute if np.abs(d_gap) < tol: ....................SS.S................................................S....................................................S......................................................../Users/stanleynwang/Programming Projects/scikit-learn/sklearn/externals/joblib/test/test_func_inspect.py:122: UserWarning: Cannot inspect object <functools.partial object at 0x104a653c0>, ignore list will not work. nose.tools.assert_equal(filter_args(ff, ['y'], (1, )), ...........................................................................................................................................................................................................................................................Exception AttributeError: AttributeError("'NoneType' object has no attribute 'tell'",) in <bound method memmap.__del__ of memmap(1.5e-323)> ignored Exception AttributeError: AttributeError("'NoneType' object has no attribute 'tell'",) in <bound method memmap.__del__ of memmap(1.5e-323)> ignored Exception AttributeError: AttributeError("'NoneType' object has no attribute 'tell'",) in <bound method memmap.__del__ of memmap(1.5e-323)> ignored /Users/stanleynwang/Programming Projects/scikit-learn/sklearn/externals/joblib/test/test_numpy_pickle.py:182: Warning: file "/var/folders/zF/zFnvGDnkF-GbddyGrBLC9k+++TI/-Tmp-/tmpbgCi7n/test.pkl764" 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(1.5e-323)> ignored ........................................................................................................................S......................................................................................................................................................................F.................................................................................................................................................................................................................................................................................................................................................................................SSS....S....S........................................................................................... ====================================================================== FAIL: test_locally_linear.test_lle_simple_grid ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/Users/stanleynwang/Programming Projects/scikit-learn/sklearn/manifold/tests/test_locally_linear.py", line 64, in test_lle_simple_grid assert_less(np.linalg.norm(X_reembedded - clf.embedding_), tol) AssertionError: 0.9331466879443665 not less than 0.1 """Fail immediately, with the given message.""" >> raise self.failureException('0.9331466879443665 not less than 0.1') ---------------------------------------------------------------------- Ran 1253 tests in 56.977s FAILED (SKIP=12, failures=1) I'm running on OS X 10.6.8 Snow Leopard, with python 2.7.3, numpy 1.6.2, scipy 0.10.1, the latest matplotlib from GitHub, and ipython 0.13. Help with this would be greatly appreciated. Thanks! Stanley Wang ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Scikit-learn-general mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/scikit-learn-general ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Scikit-learn-general mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
