{"issue":{"pull_request":{"diff_url":null,"html_url":null,"patch_url":null},"state":"open","user":{"avatar_url":"https://secure.gravatar.com/avatar/1c80795a6e2a43cdcb5f85b812c35771?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"1c80795a6e2a43cdcb5f85b812c35771","url":"https://api.github.com/users/dawenl","login":"dawenl","id":1088672},"milestone":null,"labels":[],"assignee":null,"updated_at":"2011-11-09T08:14:58Z","closed_at":null,"comments":5,"url":"https://api.github.com/repos/scikit-learn/scikit-learn/issues/435","body":"Hi all,\r\n\r\nThanks to the help this afternoon, I finally got sklearn working with my test logistic regression. However, while I run the test, I got the segmentation fault at last, here is the output (very long), it seems to me that something is not implemented yet and not sure if that's the cause of the error:\r\n\r\n\r\nRunning unit tests and doctests for sklearn\r\nNumPy version 2.0.0.dev-7297785\r\nNumPy is installed in /Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy\r\nPython 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)]\r\nnose version 1.1.2\r\n/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cross_val.py:2: UserWarning: sklearn.cross_val namespace is deprecated in version 0.9 and will be removed in version 0.11. Please use sklearn.cross_validation instead.\r\n  warnings.warn('sklearn.cross_val namespace is deprecated in version 0.9'\r\n/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/hmm.py:16: 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.\r\n  warnings.warn('sklearn.hmm is orphaned, undocumented and has known numerical'\r\n.........../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/neighbors/base.py:23: UserWarning: kneighbors: neighbor k+1 and neighbor k have the same distance: results will be dependent on data order.\r\n  warnings.warn(msg)\r\n......../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cluster/k_means_.py:219: UserWarning: Explicit initial center position passed: performing only one init in the k-means\r\n  warnings.warn('Explicit initial center position passed: '\r\n.............../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cluster/spectral.py:77: UserWarning: pyamg not available, using scipy.sparse\r\n  warnings.warn('pyamg not available, using scipy.sparse')\r\n.S...................S.S.........................FFF............/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/fastica_.py:199: UserWarning: Please note: the interface of fastica has changed: X is now assumed to be of shape [n_samples, n_features]\r\n  warnings.warn(\"Please note: the interface of fastica has changed: \"\r\n..................../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/nmf.py:237: UserWarning: Iteration limit reached in nls subproblem.\r\n  warnings.warn(\"Iteration limit reached in nls subproblem.\")\r\n.................../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/sparse_pca.py:146: RuntimeWarning: invalid value encountered in divide\r\n  U /= np.sqrt((U ** 2).sum(axis=0))\r\n......................./Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/test/test_func_inspect.py:101: UserWarning: Cannot inspect object <functools.partial object at 0x103a760a8>, ignore list will not work.\r\n  nose.tools.assert_equal(filter_args(ff, ['y'], 1),\r\n........................................................................................________________________________________________________________________________\r\ntest_memory setup\r\n________________________________________________________________________________\r\n________________________________________________________________________________\r\ntest_memory teardown\r\n________________________________________________________________________________\r\n..________________________________________________________________________________\r\ntest_memory setup\r\n________________________________________________________________________________\r\n......................................................................................................................________________________________________________________________________________\r\ntest_memory teardown\r\n________________________________________________________________________________\r\n.________________________________________________________________________________\r\nsetup numpy_pickle\r\n________________________________________________________________________________\r\n.......................................Failed to save <class 'numpy.ma.core.MaskedArray'> to .npy file:\r\nTraceback (most recent call last):\r\n  File \"/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/numpy_pickle.py\", line 62, in save\r\n    self.np.save(filename, obj)\r\n  File \"/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/lib/npyio.py\", line 434, in save\r\n    format.write_array(fid, arr)\r\n  File \"/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/lib/format.py\", line 409, in write_array\r\n    array.tofile(fp)\r\n  File \"/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/ma/core.py\", line 5380, in tofile\r\n    raise NotImplementedError(\"Not implemented yet, sorry...\")\r\nNotImplementedError: Not implemented yet, sorry...\r\n\r\n.________________________________________________________________________________\r\nteardown numpy_pickle\r\n________________________________________________________________________________\r\n...............E..................................F................/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/linear_model/least_angle.py:218: RuntimeWarning: invalid value encountered in divide\r\n  z = -coefs[n_iter, active] / least_squares\r\n....Segmentation fault: 11\r\n\r\n\r\nAny help will be appreciated. Thanks!\r\n","html_url":"https://github.com/scikit-learn/scikit-learn/issues/435","title":"Segmentation fault while running sklearn.test()","number":435,"id":2181668,"created_at":"2011-11-09T00:51:16Z"},"action":"created","comment":{"user":{"avatar_url":"https://secure.gravatar.com/avatar/5c9fb379c4e97b58960d74dcbfc5dee5?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"5c9fb379c4e97b58960d74dcbfc5dee5","url":"https://api.github.com/users/GaelVaroquaux","login":"GaelVaroquaux","id":208217},"updated_at":"2011-11-09T08:14:58Z","url":"https://api.github.com/repos/scikit-learn/scikit-learn/issues/comments/2678596","body":"You need to find where the nosetests executable is locate:\n<pre>\n$ which nosetests\n/usr/bin/nosetests\n</pre>\nThen you run gdb as such\n<pre>\n$ gdb python\n...\n(gdb) run /usr/bin/nosetests sklearn\n</pre>","id":2678596,"created_at":"2011-11-09T08:14:58Z"}}