Mailman 3 April 2008 - SciPy-User

Scipy 0.7.0dev4167 ... 44 errors?
by Joshua Lippai April 25, 2008

April 25, 2008

Hello, I was running SVN builds of SciPy retty well until just recently (I got a few filures and some errors, but apparently this is normal right now, or so I've been told). But at some recent revision, my number of errors jumped to a whopping 44, and failures to 5 from scipy.test(). Here is my output: ====================================================================== ERROR: Tests pdist(X, 'chebychev') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 538, in test_pdist_chebychev_iris Y_test1 = pdist(X, 'chebychev') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_chebychev') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 548, in test_pdist_chebychev_iris_nonC Y_test2 = pdist(X, 'test_chebychev') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'chebychev') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 517, in test_pdist_chebychev_random Y_test1 = pdist(X, 'chebychev') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_chebychev') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 527, in test_pdist_chebychev_random_nonC Y_test2 = pdist(X, 'test_chebychev') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'cityblock') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 304, in test_pdist_cityblock_iris Y_test1 = pdist(X, 'cityblock') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_cityblock') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 314, in test_pdist_cityblock_iris_nonC Y_test2 = pdist(X, 'test_cityblock') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'cityblock') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 284, in test_pdist_cityblock_random Y_test1 = pdist(X, 'cityblock') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_cityblock') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 294, in test_pdist_cityblock_random_nonC Y_test2 = pdist(X, 'test_cityblock') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'correlation') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 345, in test_pdist_correlation_iris Y_test1 = pdist(X, 'correlation') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_correlation') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 355, in test_pdist_correlation_iris_nonC Y_test2 = pdist(X, 'test_correlation') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'correlation') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 325, in test_pdist_correlation_random Y_test1 = pdist(X, 'correlation') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_correlation') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 335, in test_pdist_correlation_random_nonC Y_test2 = pdist(X, 'test_correlation') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'cosine') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 263, in test_pdist_cosine_iris Y_test1 = pdist(X, 'cosine') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_cosine') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 273, in test_pdist_cosine_iris_nonC Y_test2 = pdist(X, 'test_cosine') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'cosine') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 244, in test_pdist_cosine_random Y_test1 = pdist(X, 'cosine') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_cosine') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 253, in test_pdist_cosine_random_nonC Y_test2 = pdist(X, 'test_cosine') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'hamming') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 451, in test_pdist_dhamming_random Y_test1 = pdist(X, 'hamming') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_hamming') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 461, in test_pdist_dhamming_random_nonC Y_test2 = pdist(X, 'test_hamming') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'jaccard') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 495, in test_pdist_djaccard_random Y_test1 = pdist(X, 'jaccard') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_jaccard') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 505, in test_pdist_djaccard_random_nonC Y_test2 = pdist(X, 'test_jaccard') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'euclidean') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 185, in test_pdist_euclidean_iris Y_test1 = pdist(X, 'euclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_euclidean') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 194, in test_pdist_euclidean_iris_nonC Y_test2 = pdist(X, 'test_euclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'euclidean') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 166, in test_pdist_euclidean_random Y_test1 = pdist(X, 'euclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_euclidean') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 175, in test_pdist_euclidean_random_nonC Y_test2 = pdist(X, 'test_euclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'hamming') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 429, in test_pdist_hamming_random Y_test1 = pdist(X, 'hamming') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_hamming') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 439, in test_pdist_hamming_random_nonC Y_test2 = pdist(X, 'test_hamming') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Testing whether passing a float96 variance matrix generates an exception. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 149, in test_pdist_ivar_raises_type_error_float96 VI = numpy.zeros((10, 10), dtype=numpy.float96) AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'jaccard') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 473, in test_pdist_jaccard_random Y_test1 = pdist(X, 'jaccard') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_jaccard') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 483, in test_pdist_jaccard_random_nonC Y_test2 = pdist(X, 'test_jaccard') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'minkowski') on iris data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 408, in test_pdist_minkowski_iris Y_test1 = pdist(X, 'minkowski', 5.8) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_minkowski') [the non-C implementation] on iris data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 418, in test_pdist_minkowski_iris_nonC Y_test2 = pdist(X, 'test_minkowski', 5.8) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'minkowski') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 368, in test_pdist_minkowski_random Y_test1 = pdist(X, 'minkowski', 3.2) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_minkowski') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 378, in test_pdist_minkowski_random_nonC Y_test2 = pdist(X, 'test_minkowski', 3.2) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Testing whether passing a float96 observation array generates an exception. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 104, in test_pdist_raises_type_error_float96 X = numpy.zeros((10, 10), dtype=numpy.float96) AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'seuclidean') on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 224, in test_pdist_seuclidean_iris Y_test1 = pdist(X, 'seuclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_seuclidean') [the non-C implementation] on the Iris data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 233, in test_pdist_seuclidean_iris_nonC Y_test2 = pdist(X, 'test_sqeuclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'seuclidean') on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 205, in test_pdist_seuclidean_random Y_test1 = pdist(X, 'seuclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Tests pdist(X, 'test_sqeuclidean') [the non-C implementation] on random data. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 214, in test_pdist_seuclidean_random_nonC Y_test2 = pdist(X, 'test_sqeuclidean') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/hierarchy.py", line 1307, in pdist if X.dtype == np.float32 or X.dtype == np.float96: AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Testing whether passing a float96 variance matrix generates an exception. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 126, in test_pdist_var_raises_type_error_float96 V = numpy.zeros((10, 10), dtype=numpy.float96) AttributeError: 'module' object has no attribute 'float96' ====================================================================== ERROR: Failure: ImportError (cannot import name _bspline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/loader.py", line 364, in loadTestsFromName File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/importer.py", line 39, in importFromPath File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.10.1-py2.5.egg/nose/importer.py", line 84, in importFromDir File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_bspline.py", line 9, in <module> import scipy.stats.models.bspline as B File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/bspline.py", line 23, in <module> from scipy.stats.models import _bspline ImportError: cannot import name _bspline ====================================================================== ERROR: test_factor3 (test_formula.TestFormula) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py", line 231, in test_factor3 m = fac.main_effect(reference=1) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/formula.py", line 273, in main_effect reference = names.index(reference) ValueError: list.index(x): x not in list ====================================================================== ERROR: test_factor4 (test_formula.TestFormula) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py", line 239, in test_factor4 m = fac.main_effect(reference=2) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/formula.py", line 273, in main_effect reference = names.index(reference) ValueError: list.index(x): x not in list ====================================================================== ERROR: test_huber (test_scale.TestScale) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_scale.py", line 35, in test_huber m = scale.huber(X) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py", line 82, in __call__ for donothing in self: File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py", line 102, in next scale = N.sum(subset * (a - mu)**2, axis=self.axis) / (self.n * Huber.gamma - N.sum(1. - subset, axis=self.axis) * Huber.c**2) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/fromnumeric.py", line 930, in sum return sum(axis, dtype, out) TypeError: only length-1 arrays can be converted to Python scalars ====================================================================== ERROR: test_huberaxes (test_scale.TestScale) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_scale.py", line 40, in test_huberaxes m = scale.huber(X, axis=0) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py", line 82, in __call__ for donothing in self: File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/robust/scale.py", line 102, in next scale = N.sum(subset * (a - mu)**2, axis=self.axis) / (self.n * Huber.gamma - N.sum(1. - subset, axis=self.axis) * Huber.c**2) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/fromnumeric.py", line 930, in sum return sum(axis, dtype, out) TypeError: only length-1 arrays can be converted to Python scalars ====================================================================== FAIL: Testing whether passing a float32 variance matrix generates an exception. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 144, in test_pdist_ivar_raises_type_error_float32 self.fail("float32 matrices should generate an error in pdist('mahalanobis').") AssertionError: float32 matrices should generate an error in pdist('mahalanobis'). ====================================================================== FAIL: Testing whether passing a float32 variance matrix generates an exception. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 121, in test_pdist_var_raises_type_error_float32 self.fail("float32 V matrices should generate an error in pdist('seuclidean').") AssertionError: float32 V matrices should generate an error in pdist('seuclidean'). ====================================================================== FAIL: test_texture2 (test_segment.TestSegment) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/tests/test_segment.py", line 152, in test_texture2 assert_array_almost_equal(tem0, truth_tem0, decimal=6) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 255, in assert_array_almost_equal header='Arrays are not almost equal') File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 240, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 66.6666666667%) x: array([ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.91816598e-01, 1.02515288e-01, 9.30087343e-02,... y: array([ 0. , 0. , 0. , 0. , 0. , 0. , 0.13306101, 0.08511007, 0.05084148, 0.07550675, 0.4334695 , 0.03715914, 0.00289055, 0.02755581, 0.48142046, 0.03137803, 0.00671277, 0.51568902, 0.01795249, 0.49102375, 1. ], dtype=float32) ====================================================================== FAIL: test_gammaincinv (test_basic.TestGamma) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/tests/test_basic.py", line 1056, in test_gammaincinv assert_almost_equal(0.05, x, decimal=10) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/testing/utils.py", line 158, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: ACTUAL: 0.050000000000000003 DESIRED: 0.0 ====================================================================== FAIL: test_namespace (test_formula.TestFormula) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/models/tests/test_formula.py", line 119, in test_namespace self.assertEqual(xx.namespace, Y.namespace) AssertionError: {} != {'Y': array([ 0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98]), 'X': array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])} ====================================================================== SKIP: Getting factors of complex matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Getting factors of real matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Getting factors of complex matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Getting factors of real matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Prefactorize (with UMFPACK) matrix for solving with multiple rhs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Prefactorize matrix for solving with multiple rhs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Solve with UMFPACK: double precision complex ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Solve: single precision complex ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Solve with UMFPACK: double precision, sparse rhs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Solve with UMFPACK: double precision ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ====================================================================== SKIP: Solve: single precision ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ---------------------------------------------------------------------- Ran 2116 tests in 23.236s FAILED (failures=5, errors=44) Is this some kind of issue with a recent revision to the scipy tests, or is it all me? Josh

3 2

Re: [SciPy-user] Scipy 0.7.0dev4167 ... 44 errors?
by Damian Eads April 25, 2008

April 25, 2008

I wrote the hierarchy tests last week. The number of errors in scipy/cluster/hierarchy* may sound overwhelming but most of them seem to be caused by the same problem -- numpy.float96 not being defined. Is it sometimes the case this type code is undefined, maybe because numpy was compiled on a machine not supporting 96-bit floats? Damian Joshua Lippai wrote: > From: *Joshua Lippai* <discerptor(a)gmail.com <mailto:discerptor@gmail.com>> > Date: Wed, Apr 23, 2008 at 12:26 PM > To: SciPy Users List <scipy-user(a)scipy.org <mailto:scipy-user@scipy.org>> > > > Hello, > > I was running SVN builds of SciPy retty well until just recently (I > got a few filures and some errors, but apparently this is normal right > now, or so I've been told). But at some recent revision, my number of > errors jumped to a whopping 44, and failures to 5 from scipy.test(). > Here is my output:

1 0

Large matrix support
by Dinesh B Vadhia April 25, 2008

April 25, 2008

I'm (sadly or otherwise) developing using Python w/ Numpy/Scipy on a Windows XP machine. The Python code will be moved onto a Linux server eventually. My matrix sizes can be large ie. > minimum 20,000 rows x 1m columns. When just creating these data sets using Python/Numpy/Scipy, I get pythonw.exe errors and the program aborts. I guess the Microsoft 32K limit has been reached somewhere. I haven't got any Python program to run with these data sets because of 'not enough memory' errors. I'm waiting for the int8 support in the sparse library to hopefully resolve that issue. Assuming, that the int8 support were available, will Python in a Windows environment allow the creation of these large matrices let alone run Python programs against them? Btw, I have sufficient memory on my computer. Btw btw, I'm not setup to create Numpy/Scipy svn builds but if some kind soul(s) were able to provide access to the latest pre-compiled Windows builds I'll happily be a guinea pig to test Numpy/Scipy against these large matrix sizes. Cheers Dinesh

2 1

Random sparse matrices
by Mico Filós April 25, 2008

April 25, 2008

Dear all, Is there any function similar to octave's 'sprandn', which generates a sparse random matrix with values normally distributed? http://octave.sourceforge.net/index/f/sprand.html Thanks a lot in advance

7 15

Matrix, Sparse problem with svn 4167
by Dinesh B Vadhia April 25, 2008

April 25, 2008

I have a working program with b=Ax, where A is a large sparse matrix. However, I need the int8 support in the sparse library to utilize larger matrices. I managed to get hold of a scipy svn 4167 build and b=Ax now returns garbage results. Nothing was changed in the program except replacing getrow with .todense() and I checked these to make sure the right rows were being picked up. I wish could point out where exactly the problem lies but there was no Traceback just the wrong results but it can safely be assumed it is with the numpy/scipy matrix support. Any ideas? Dinesh

2 1

Re: [SciPy-user] failure to build scipy on RHEL5
by Michael Hearne April 25, 2008

April 25, 2008

Paul (or anyone) - You're right, there are other dependencies: error: Failed dependencies: libamd.so.2()(64bit) is needed by python-scipy-0.6.0-3.el5.x86_64 libfftw3.so.3()(64bit) is needed by python-scipy-0.6.0-3.el5.x86_64 libumfpack.so.5()(64bit) is needed by python-scipy-0.6.0-3.el5.x86_64 I did some searching around and found that libamd and libumfpack are both included in something called SparseSuite (http://www.cise.ufl.edu/research/sparse/SuiteSparse/ ). I found links to the RPM for this package here: http://rpm.pbone.net/index.php3/stat/4/idpl/4852092/com/suitesparse-3.0.0-1… but unfortunately can't connect to any of the mirrors. Does anyone have any tips or pre-made RPMs for SparseSuite or the two libraries mentioned above? I haven't even started to look for the FFT library yet... --Mike On Apr 24, 2008, at 7:31 PM, Paul Barrett wrote: > Mike, > > Attached are the following RPMs: > > atlas, blas, lapack, python-numpy, python-scipy > > You may need some additional packages such as fftw3, etc. which are > readily available in one or more repositories. > > I'll send the devel RPMs in the next email. > > I hope that you get them. > > -- Paul > > On Thu, Apr 24, 2008 at 6:22 PM, Michael Hearne <mhearne(a)usgs.gov> > wrote: >> Yes. >> >> >> >> On Apr 24, 2008, at 2:27 PM, Paul Barrett wrote: >> Mike, >> >> Are you on a 64 bit platform? >> >> -- Paul >> >> On Thu, Apr 24, 2008 at 12:52 PM, Michael Hearne <mhearne(a)usgs.gov> >> wrote: >> Paul - I apologize if you get two responses - it's not clear if my >> email >> client actually delivered another email I just sent on this topic. >> >> In answer to your offer - yes, that would be great if I could get >> the RPMs, >> as I am completely unable to compile scipy on my own. I'm using >> f77, and >> getting complaints about not having a Fortran 90 compiler, and not >> having >> compiled with LAPACK with -fPIC (which I certainly _tried_ to do). >> >> Anyway, if you have time to put them on EPEL, that would help me and >> hopefully other frustrated RHEL users out there. Otherwise, let me >> know the >> best way for me to get the files. >> >> Thanks, >> >> Mike >> >> >> >> On Apr 23, 2008, at 4:17 PM, Paul Barrett wrote: >> Mike, >> >> I have numpy, scipy, and matplotlib RPMs for EL5 x86_64, if you want >> them. I also think that I have the i386 ones too, but the SRPMs are >> of course available. >> >> I've been meaning to offer them to the EPEL repository, but I haven't >> made the time. >> >> -- Paul >> >> >> On Wed, Apr 23, 2008 at 5:59 PM, Robert Kern >> <robert.kern(a)gmail.com> wrote: >> On Wed, Apr 23, 2008 at 4:53 PM, Michael Hearne <mhearne(a)usgs.gov> >> wrote: >> >> Wasn't sure how far back to go, so here's several more lines' worth: >> >> Here's the important one: >> >> >> /usr/bin/ld: /usr/local/lib/libfblas.a(cgemm.o): relocation >> R_X86_64_32 against `a local symbol' can not be used when making a >> shared object; recompile with -fPIC >> /usr/local/lib/libfblas.a: could not read symbols: Bad value >> >> You need to compile BLAS to be relocatable using the -fPIC flag to >> the >> compilation flags. If you are following the directions on that wiki >> strictly, replace this line: >> >> g77 -fno-second-underscore -O2 -c *.f >> >> with this line: >> >> g77 -fPIC -fno-second-underscore -O2 -c *.f >> >> >> >> -- >> Robert Kern >> >> "I have come to believe that the whole world is an enigma, a harmless >> enigma that is made terrible by our own mad attempt to interpret it >> as >> though it had an underlying truth." >> -- Umberto Eco >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> >> >> >> ------------------------------------------------------ >> Michael Hearne >> mhearne(a)usgs.gov >> (303) 273-8620 >> USGS National Earthquake Information Center >> 1711 Illinois St. Golden CO 80401 >> Senior Software Engineer >> Synergetics, Inc. >> ------------------------------------------------------ >> >> >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> >> >> >> >> >> ------------------------------------------------------ >> Michael Hearne >> mhearne(a)usgs.gov >> (303) 273-8620 >> USGS National Earthquake Information Center >> 1711 Illinois St. Golden CO 80401 >> Senior Software Engineer >> Synergetics, Inc. >> ------------------------------------------------------ >> >> > < > atlas > -3.6.0 > -12 > .el5 > .x86_64 > .rpm > ><blas-3.1.1-2.el5.x86_64.rpm><lapack-3.1.1-2.el5.x86_64.rpm><python- > numpy-1.0.4-1.el5.x86_64.rpm><python-scipy-0.6.0-3.el5.x86_64.rpm> ------------------------------------------------------ Michael Hearne mhearne(a)usgs.gov (303) 273-8620 USGS National Earthquake Information Center 1711 Illinois St. Golden CO 80401 Senior Software Engineer Synergetics, Inc. ------------------------------------------------------

1 0

Re: [SciPy-user] failure to build scipy on RHEL5
by Michael Hearne April 25, 2008

April 25, 2008

Paul - Thanks! I took a first crack at installing these, and started with BLAS. When I do "sudo rpm -i blas-3.1.1-2.el5.x86_64.rpm", I get a bunch of conflicts... I then tried "sudo rpm -q blas" and was returned: blas-3.0-37.el5 blas-3.0-37.el5 I'm not terribly familiar with RH, as I use Ubuntu at home, does this mean I have two instances of BLAS 3.0 already installed? If so, is it safe to use rpm to remove them? --Mike On Apr 24, 2008, at 7:31 PM, Paul Barrett wrote: > Mike, > > Attached are the following RPMs: > > atlas, blas, lapack, python-numpy, python-scipy > > You may need some additional packages such as fftw3, etc. which are > readily available in one or more repositories. > > I'll send the devel RPMs in the next email. > > I hope that you get them. > > -- Paul > > On Thu, Apr 24, 2008 at 6:22 PM, Michael Hearne <mhearne(a)usgs.gov> > wrote: >> Yes. >> >> >> >> On Apr 24, 2008, at 2:27 PM, Paul Barrett wrote: >> Mike, >> >> Are you on a 64 bit platform? >> >> -- Paul >> >> On Thu, Apr 24, 2008 at 12:52 PM, Michael Hearne <mhearne(a)usgs.gov> >> wrote: >> Paul - I apologize if you get two responses - it's not clear if my >> email >> client actually delivered another email I just sent on this topic. >> >> In answer to your offer - yes, that would be great if I could get >> the RPMs, >> as I am completely unable to compile scipy on my own. I'm using >> f77, and >> getting complaints about not having a Fortran 90 compiler, and not >> having >> compiled with LAPACK with -fPIC (which I certainly _tried_ to do). >> >> Anyway, if you have time to put them on EPEL, that would help me and >> hopefully other frustrated RHEL users out there. Otherwise, let me >> know the >> best way for me to get the files. >> >> Thanks, >> >> Mike >> >> >> >> On Apr 23, 2008, at 4:17 PM, Paul Barrett wrote: >> Mike, >> >> I have numpy, scipy, and matplotlib RPMs for EL5 x86_64, if you want >> them. I also think that I have the i386 ones too, but the SRPMs are >> of course available. >> >> I've been meaning to offer them to the EPEL repository, but I haven't >> made the time. >> >> -- Paul >> >> >> On Wed, Apr 23, 2008 at 5:59 PM, Robert Kern >> <robert.kern(a)gmail.com> wrote: >> On Wed, Apr 23, 2008 at 4:53 PM, Michael Hearne <mhearne(a)usgs.gov> >> wrote: >> >> Wasn't sure how far back to go, so here's several more lines' worth: >> >> Here's the important one: >> >> >> /usr/bin/ld: /usr/local/lib/libfblas.a(cgemm.o): relocation >> R_X86_64_32 against `a local symbol' can not be used when making a >> shared object; recompile with -fPIC >> /usr/local/lib/libfblas.a: could not read symbols: Bad value >> >> You need to compile BLAS to be relocatable using the -fPIC flag to >> the >> compilation flags. If you are following the directions on that wiki >> strictly, replace this line: >> >> g77 -fno-second-underscore -O2 -c *.f >> >> with this line: >> >> g77 -fPIC -fno-second-underscore -O2 -c *.f >> >> >> >> -- >> Robert Kern >> >> "I have come to believe that the whole world is an enigma, a harmless >> enigma that is made terrible by our own mad attempt to interpret it >> as >> though it had an underlying truth." >> -- Umberto Eco >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> >> >> >> ------------------------------------------------------ >> Michael Hearne >> mhearne(a)usgs.gov >> (303) 273-8620 >> USGS National Earthquake Information Center >> 1711 Illinois St. Golden CO 80401 >> Senior Software Engineer >> Synergetics, Inc. >> ------------------------------------------------------ >> >> >> _______________________________________________ >> SciPy-user mailing list >> SciPy-user(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-user >> >> >> >> >> >> >> ------------------------------------------------------ >> Michael Hearne >> mhearne(a)usgs.gov >> (303) 273-8620 >> USGS National Earthquake Information Center >> 1711 Illinois St. Golden CO 80401 >> Senior Software Engineer >> Synergetics, Inc. >> ------------------------------------------------------ >> >> > < > atlas > -3.6.0 > -12 > .el5 > .x86_64 > .rpm > ><blas-3.1.1-2.el5.x86_64.rpm><lapack-3.1.1-2.el5.x86_64.rpm><python- > numpy-1.0.4-1.el5.x86_64.rpm><python-scipy-0.6.0-3.el5.x86_64.rpm> ------------------------------------------------------ Michael Hearne mhearne(a)usgs.gov (303) 273-8620 USGS National Earthquake Information Center 1711 Illinois St. Golden CO 80401 Senior Software Engineer Synergetics, Inc. ------------------------------------------------------

2 1

remove duplicate points...
by fred April 24, 2008

April 24, 2008

Hi, I have array of 3D points: [x0, y0, z0, v0] [x1, y1, z1, v1] ... [xn, yn, zn, vn] This array have duplicate elements (points), by construction. How could I remove these duplicate elements ? numpy.unique seems to not fit my needs... TIA. Cheers, -- Fred

11 16

Sparse matrix todense
by Dinesh B Vadhia April 24, 2008

April 24, 2008

Hi! The following code worked until I installed the latest svn. I want to select a particular row (eg. row=1818) from the sparse matrix A: > import numpy > import scipy > from scipy import sparse <snip> > A = sparse.csr_matrix(A) > q[0,:] = sparse.csr_matrix.todense(sparse.csr_matrix.getrow(A, 1818)) The Traceback is: Traceback (most recent call last): File "C:\...\.py", line 157, in <module> q[0,:] = sparse.csr_matrix.todense(sparse.csr_matrix.getrow(A, 1818)) File "C:\Python25\Lib\site-packages\scipy\sparse\base.py", line 357, in getrow a = csr_matrix((1, m), dtype=self.dtype) NameError: global name 'csr_matrix' is not defined Thanks! Dinesh

2 1

problem with UMFPACK in scipy.test
by Johann Cohen-Tanugi April 24, 2008

April 24, 2008

hello, I have compiled and built UMFPACK, following the wiki, and when configuring scipy I read : umfpack_info: amd_info: libraries amd not found in /usr/local/lib FOUND: libraries = ['amd'] library_dirs = ['/usr/lib'] FOUND: libraries = ['umfpack', 'amd'] library_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Lib/', '/usr/lib'] swig_opts = ['-I/data1/sources/MATHSTUFF/UMFPACK/Include'] define_macros = [('SCIPY_UMFPACK_H', None)] include_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Include'] I would infer from that that UMFPACK was correctly found, but after building scipy from svn, I get : In [4]: scipy.test(verbose=2) <lots of stuff> ====================================================================== SKIP: Getting factors of complex matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled <several other outputs of the same kind> ====================================================================== SKIP: Solve: single precision ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/testing/decorators.py", line 81, in skipper raise nose.SkipTest, msg SkipTest: UMFPACK appears not to be compiled ---------------------------------------------------------------------- Ran 1524 tests in 39.269s FAILED (failures=5, errors=12) What does that mean? I noticed that when building UMFPACK I put -fPIC in the UFConfig.mk but it does not seem to be honored. For instance : gcc -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I../Include -I../Source -I../../AMD/Include -I../../UFconfig -DDINT -c ../Source/umfpack_qsymbolic.c -o umfpack_di_qsymbolic.o Is that related? thanks in advance, Johann

2 2