Hi, I am using Python.org amd64 python build on windows 7 64 bit. I am using numpy and scipy builds from here: http://www.lfd.uci.edu/~gohlke/pythonlibs/ I get many errors in scipy test (none for numpy). Particularly in scipy.sparse.linalg which I need to use (and in my code it appears spsolve is giving incorrect results). Is there a better 64 bit windows build to use?
scipy.test() Running unit tests for scipy NumPy version 1.4.1 NumPy is installed in C:\Python26\lib\site-packages\numpy SciPy version 0.8.0b1 SciPy is installed in C:\Python26\lib\site-packages\scipy Python version 2.6.5 (r265:79096, Mar 19 2010, 18:02:59) [MSC v.1500 64 bit (AMD64)] nose version 0.11.3 ........................................................................................................................ ............................E....................................F...................................................... ..............................C:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py:639: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) .....C:\Python26\lib\site-packages\scipy\interpolate\fitpack2.py:580: UserWarning: The required storage space exceeds the available storage space: nxest or nyest too small, or s too small. The weighted least-squares spline corresponds to the current set of knots. warnings.warn(message) ...........................................K..K......................................................................... ........................................................................................................................ ........................................................................................................................ EC:\Python26\lib\site-packages\numpy\lib\utils.py:140: DeprecationWarning: `write_array` is deprecated!
This function is replaced by numpy.savetxt which allows the same functionality through a different syntax. warnings.warn(depdoc, DeprecationWarning) C:\Python26\lib\site-packages\numpy\lib\utils.py:140: DeprecationWarning: `read_array` is deprecated! The functionality of read_array is in numpy.loadtxt which allows the same functionality using different syntax. warnings.warn(depdoc, DeprecationWarning) ...........................................Exception AttributeError: "'netcdf_file' object has no attribute 'mode'" in < bound method netcdf_file.close of <scipy.io.netcdf.netcdf_file object at 0x000000000C64D6D8>> ignored ............C:\Python26\lib\site-packages\numpy\lib\utils.py:140: DeprecationWarning: `npfile` is deprecated! You can achieve the same effect as using npfile using numpy.save and numpy.load. You can use memory-mapped arrays and data-types to map out a file format for direct manipulation in NumPy. warnings.warn(depdoc, DeprecationWarning) .........C:\Python26\lib\site-packages\scipy\io\wavfile.py:30: WavFileWarning: Unfamiliar format bytes warnings.warn("Unfamiliar format bytes", WavFileWarning) C:\Python26\lib\site-packages\scipy\io\wavfile.py:120: WavFileWarning: chunk not understood warnings.warn("chunk not understood", WavFileWarning) ........................................................................................................................ .......................................................................................................SSSSSS......SSSSS S......SSSS...............................................................S............................................. ........................................................................................................................ ..............................................E......................................................................... ........................................................................................................................ ....SSS.........S....................................................................................................... .............................................................F.......................................................... ........................................................................................................................ .....................................................FFF.....................................................C:\Python26 \lib\site-packages\scipy\signal\filter_design.py:247: BadCoefficients: Badly conditioned filter coefficients (numerator) : the results may be meaningless "results may be meaningless", BadCoefficients) 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.............................S.......................................................................................... ...........................................................................................C:\Python26\lib\site-packages \scipy\stats\morestats.py:702: UserWarning: Ties preclude use of exact statistic. warnings.warn("Ties preclude use of exact statistic.") ........................................................................................................................ ........................................................................................................................ ....................................................error removing c:\users\robince\appdata\local\temp\tmpr3s_aecat_test : c:\users\robince\appdata\local\temp\tmpr3s_aecat_test: The directory is not empty .................................................................................................. ====================================================================== ERROR: Testing that kmeans2 init methods work. ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\cluster\tests\test_vq.py", line 166, in test_kmeans2_init kmeans2(data, 3, minit = 'points') File "C:\Python26\lib\site-packages\scipy\cluster\vq.py", line 671, in kmeans2 clusters = init(data, k) File "C:\Python26\lib\site-packages\scipy\cluster\vq.py", line 523, in _kpoints p = np.random.permutation(n) File "mtrand.pyx", line 4231, in mtrand.RandomState.permutation (build\scons\numpy\random\mtrand\mtrand.c:18669) File "mtrand.pyx", line 4174, in mtrand.RandomState.shuffle (build\scons\numpy\random\mtrand\mtrand.c:18261) TypeError: len() of unsized object ====================================================================== ERROR: test_basic (test_array_import.TestNumpyio) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\io\tests\test_array_import.py", line 29, in test_basic b = numpyio.fread(fid,1000000,N.Int16,N.Int) MemoryError ====================================================================== ERROR: test_decomp.test_lapack_misaligned(<function solve at 0x0000000006366438>, (array([[ 1.734e-255, 8.189e-217, 4.025e-178, 1.903e-139, 9.344e-101, ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\linalg\tests\test_decomp.py", line 1074, in check_lapack_misaligned func(*a,**kwargs) File "C:\Python26\lib\site-packages\scipy\linalg\basic.py", line 49, in solve a1, b1 = map(asarray_chkfinite,(a,b)) File "C:\Python26\lib\site-packages\numpy\lib\function_base.py", line 586, in asarray_chkfinite raise ValueError, "array must not contain infs or NaNs" ValueError: array must not contain infs or NaNs ====================================================================== ERROR: Regression test for #880: empty array for zi crashes. ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\signal\tests\test_signaltools.py", line 422, in test_empty_zi y, zf = lfilter(b, a, x, zi=zi) File "C:\Python26\lib\site-packages\scipy\signal\signaltools.py", line 610, in lfilter return sigtools._linear_filter(b, a, x, axis, zi) TypeError: array cannot be safely cast to required type ====================================================================== ERROR: test_linsolve.TestSplu.test_lu_refcount ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 122, in test_lu_refcount lu = splu(a_) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_linsolve.TestSplu.test_spilu_smoketest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 60, in test_spilu_smokete st lu = spilu(self.A, drop_tol=1e-2, fill_factor=5) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 245, in spilu ilu=True, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_linsolve.TestSplu.test_splu_basic ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 87, in test_splu_basic lu = splu(a_) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_linsolve.TestSplu.test_splu_perm ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 100, in test_splu_perm lu = splu(a_) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_linsolve.TestSplu.test_splu_smoketest ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 53, in test_splu_smoketes t lu = splu(self.A) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: Check that QMR works with left and right preconditioners ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\linalg\isolve\tests\test_iterative.py", line 161, in test_leftright_p recond L_solver = splu(L) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_preconditioner (test_lgmres.TestLGMRES) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\linalg\isolve\tests\test_lgmres.py", line 38, in test_preconditioner pc = splu(Am.tocsc()) File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", line 173, in splu ilu=False, options=_options) RuntimeError: Factor is exactly singular ====================================================================== ERROR: test_mu (test_base.TestBSR) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py", line 966, in test_mu D1 = A * B.T File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py", line 319, in __mul__ return N.dot(self, asmatrix(other)) TypeError: array cannot be safely cast to required type ====================================================================== ERROR: test_mu (test_base.TestCSC) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py", line 966, in test_mu D1 = A * B.T File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py", line 319, in __mul__ return N.dot(self, asmatrix(other)) TypeError: array cannot be safely cast to required type ====================================================================== ERROR: test_mu (test_base.TestCSR) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py", line 966, in test_mu D1 = A * B.T File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py", line 319, in __mul__ return N.dot(self, asmatrix(other)) TypeError: array cannot be safely cast to required type ====================================================================== ERROR: test_mu (test_base.TestDIA) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py", line 966, in test_mu D1 = A * B.T File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py", line 319, in __mul__ return N.dot(self, asmatrix(other)) TypeError: array cannot be safely cast to required type ====================================================================== ERROR: test_mu (test_base.TestLIL) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\tests\test_base.py", line 966, in test_mu D1 = A * B.T File "C:\Python26\lib\site-packages\numpy\matrixlib\defmatrix.py", line 319, in __mul__ return N.dot(self, asmatrix(other)) TypeError: array cannot be safely cast to required type ====================================================================== FAIL: test_complex (test_basic.TestLongDoubleFailure) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\fftpack\tests\test_basic.py", line 527, in test_complex np.longcomplex) AssertionError: Type <type 'numpy.complex128'> not supported but does not fail ====================================================================== FAIL: extrema 3 ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\ndimage\tests\test_ndimage.py", line 3149, in test_extrema03 self.failUnless(numpy.all(output1[2] == output4)) AssertionError ====================================================================== FAIL: test_lorentz (test_odr.TestODR) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py", line 292, in test_lorentz 3.7798193600109009e+00]), File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 765, in assert_array_almost_equal header='Arrays are not almost equal') File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 609, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.00000000e+03, 1.00000000e-01, 3.80000000e+00]) y: array([ 1.43067808e+03, 1.33905090e-01, 3.77981936e+00]) ====================================================================== FAIL: test_multi (test_odr.TestODR) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py", line 188, in test_multi 0.5101147161764654, 0.5173902330489161]), File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 765, in assert_array_almost_equal header='Arrays are not almost equal') File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 609, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4. , 2. , 7. , 0.4, 0.5]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ====================================================================== FAIL: test_pearson (test_odr.TestODR) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\odr\tests\test_odr.py", line 235, in test_pearson np.array([ 5.4767400299231674, -0.4796082367610305]), File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 765, in assert_array_almost_equal header='Arrays are not almost equal') File "C:\Python26\lib\site-packages\numpy\testing\utils.py", line 609, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1., 1.]) y: array([ 5.47674003, -0.47960824]) ====================================================================== FAIL: test_twodiags (test_linsolve.TestLinsolve) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\scipy\sparse\linalg\dsolve\tests\test_linsolve.py", line 39, in test_twodiags assert( norm(b - Asp*x) < 10 * cond_A * eps ) AssertionError ====================================================================== FAIL: test_kdtree.test_vectorization.test_single_query ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\spatial\tests\test_kdtree.py", line 154, in test_single_query assert isinstance(i,int) AssertionError ====================================================================== FAIL: test_data.test_boost(<Data for arccosh: acosh_data_ipp-acosh_data>,) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\special\tests\test_data.py", line 205, in _test_factory test.check(dtype=dtype) File "C:\Python26\lib\site-packages\scipy\special\tests\testutils.py", line 187, in check assert False, "\n".join(msg) AssertionError: Max |adiff|: 1.77636e-15 Max |rdiff|: 1.09352e-13 Bad results for the following points (in output 0): 1.0000014305114746 => 0.0016914556651294794 != 0.0016914556651292944 (rdiff 1.093 5249113484058e-13) 1.000007152557373 => 0.0037822080446614169 != 0.0037822080446612951 (rdiff 3.222 0418006721235e-14) 1.0000138282775879 => 0.005258943946801071 != 0.0052589439468011014 (rdiff 5.772 5773723182603e-15) 1.0000171661376953 => 0.0058593666181291238 != 0.0058593666181292027 (rdiff 1.347 0725302071254e-14) 1.0000600814819336 => 0.01096183199218881 != 0.010961831992188852 (rdiff 3.798 0296955025714e-15) 1.0001168251037598 => 0.015285472131830317 != 0.015285472131830425 (rdiff 7.036 2795851489781e-15) 1.0001487731933594 => 0.017249319093529933 != 0.017249319093529877 (rdiff 3.218 1647826365358e-15) 1.0003981590270996 => 0.028218171738655599 != 0.028218171738655373 (rdiff 7.991 8023735059643e-15) 1.000638484954834 => 0.035732814682314498 != 0.035732814682314568 (rdiff 1.941 8828227213605e-15) 1.0010714530944824 => 0.046287402472878984 != 0.046287402472878776 (rdiff 4.497 2672043800306e-15) 1.0049939155578613 => 0.099897593086028066 != 0.099897593086027803 (rdiff 2.639 4826962588157e-15) 1.024169921875 => 0.21942279004958387 != 0.21942279004958354 (rdiff 1.517 9230348510424e-15) ====================================================================== FAIL: test_data.test_boost(<Data for arctanh: atanh_data_ipp-atanh_data>,) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python26\lib\site-packages\nose-0.11.3-py2.6.egg\nose\case.py", line 186, in runTest self.test(*self.arg) File "C:\Python26\lib\site-packages\scipy\special\tests\test_data.py", line 205, in _test_factory test.check(dtype=dtype) File "C:\Python26\lib\site-packages\scipy\special\tests\testutils.py", line 187, in check assert False, "\n".join(msg) AssertionError: Max |adiff|: 6.39488e-12 Max |rdiff|: 1.01982e-12 Bad results for the following points (in output 0): -0.99999284744262695 => -6.2705920974721474 != -6.2705920974657525 (rdiff 1.019 8214973073088e-12) -0.99998283386230469 => -5.832855225376532 != -5.832855225378502 (rdiff 3.377 3849320373679e-13) ---------------------------------------------------------------------- Ran 4410 tests in 29.842s FAILED (KNOWNFAIL=11, SKIP=38, errors=16, failures=9) <nose.result.TextTestResult run=4410 errors=16 failures=9>