Alright, I tried running it without any argument in the parentheses, and tests run, but with a failure and lots of errors.

...

...

scipy.test() /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4: DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', DeprecationWarning) /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/splinalg/__init__.py:3: DeprecationWarning: scipy.splinalg has moved to scipy.sparse.linalg warn('scipy.splinalg has moved to scipy.sparse.linalg', DeprecationWarning) .../Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/cluster/vq.py:477: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. " exception raised as expected: One of the clusters is empty. Re-run kmean with a different initialization. ................................................................/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458: 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) ........................................... Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. ./Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111: DeprecationWarning: write_array is deprecated warnings.warn(str1, DeprecationWarning) /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111: DeprecationWarning: read_array is deprecated warnings.warn(str1, DeprecationWarning) ..................../Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/utils.py:111: DeprecationWarning: npfile is deprecated warnings.warn(str1, DeprecationWarning) ............................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 ..

WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** ..........................................NO ATLAS INFO AVAILABLE ......................................... **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** ...............................................................................................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 .... **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** ...Result may be inaccurate, approximate err = 1.23518201169e-08 ...Result may be inaccurate, approximate err = 7.27595761418e-12 .....SSS........................................................................................................................................................................................................................................................................................................................................................................................................./Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/ndimage/_segmenter.py:35: UserWarning: The segmentation code is under heavy development and therefore the public API will change in the future. The NIPY group is actively working on this code, and has every intention of generalizing this for the Scipy community. Use this module minimally, if at all, until it this warning is removed. warnings.warn(_msg, UserWarning) EEE............................................SSSSSSSSSSS..... _naupd: Number of update iterations taken ----------------------------------------- 1 - 1: 12 _naupd: Number of wanted "converged" Ritz values ------------------------------------------------ 1 - 1: 4 _naupd: Real part of the final Ritz values ------------------------------------------ 1 - 4: 1.033D+00 7.746D-01 5.164D-01 2.582D-01 _naupd: Imaginary part of the final Ritz values ----------------------------------------------- 1 - 4: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 _naupd: Associated Ritz estimates --------------------------------- 1 - 4: 3.197D-15 3.493D-18 2.179D-23 2.140D-26 ============================================= = Nonsymmetric implicit Arnoldi update code = = Version Number: 2.4 = = Version Date: 07/31/96 = ============================================= = Summary of timing statistics = ============================================= Total number update iterations = 12 Total number of OP*x operations = 55 Total number of B*x operations = 0 Total number of reorthogonalization steps = 54 Total number of iterative refinement steps = 0 Total number of restart steps = 0 Total time in user OP*x operation = 0.001100 Total time in user B*x operation = 0.000000 Total time in Arnoldi update routine = 0.002971 Total time in naup2 routine = 0.002768 Total time in basic Arnoldi iteration loop = 0.001710 Total time in reorthogonalization phase = 0.000257 Total time in (re)start vector generation = 0.000004 Total time in Hessenberg eig. subproblem = 0.000693 Total time in getting the shifts = 0.000045 Total time in applying the shifts = 0.000210 Total time in convergence testing = 0.000023 Total time in computing final Ritz vectors = 0.000000 ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................0.2 0.2 0.2 ......0.2 ..0.2 0.2 0.2 0.2 0.2 ...................E........EE....F......................EE..................................................................................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. .........warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ...warning: specified build_dir '..' does not exist or is not writable. Trying default locations ..warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ...warning: specified build_dir '..' does not exist or is not writable. Trying default locations ............................building extensions here: /Users/Josh/.python25_compiled/m0 ................................................................................................ ====================================================================== ERROR: test1 (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 12, in test1 image = get_slice(filename) NameError: global name 'get_slice' is not defined ====================================================================== ERROR: test2 (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 27, in test2 sourceImage, labeledMask, ROIList = segment_regions(filename) NameError: global name 'segment_regions' is not defined ====================================================================== ERROR: test3 (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 37, in test3 regionMask, numberRegions = grow_regions(filename) NameError: global name 'grow_regions' is not defined ====================================================================== 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 addr.filename, addr.module) 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 return self.importFromDir(dir_path, fqname) 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 mod = load_module(part_fqname, fh, filename, desc) 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: 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: test_bytescale (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- 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: Need to import PIL for this test ====================================================================== SKIP: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- 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: Need to import PIL for this test ====================================================================== SKIP: Test generator for parametric tests ---------------------------------------------------------------------- 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/case.py", line 203, in runTest self.test(*self.arg) 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: Need to import PIL for this test ====================================================================== 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 2022 tests in 19.838s FAILED (failures=1, errors=8) Should I just try a clean install of SciPy at this point? Josh On Fri, Mar 21, 2008 at 1:38 PM, Robert Kern <robert.kern@gmail.com> wrote:

On Fri, Mar 21, 2008 at 3:30 PM, Joshua Lippai <discerptor@gmail.com> wrote:

...

Hello all,

Last night I tried installing scipy (on OS X 10.5.2) and I was surprised to find that nose is now required to run scipy.test. I installed it successfully through easy_install, but now it still won't run the test, instead producing the following error:

...

...

...

scipy.test(1,10) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/nosetester.py", line 115, in test argv = self._test_argv(label, verbose, extra_argv) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/testing/nosetester.py", line 98, in _test_argv raise TypeError, 'Selection label should be a string' TypeError: Selection label should be a string

Has anyone experienced this as well or now what's going on and how to fix it so I can run scipy.test? Much thanks in advance.

In [6]: scipy.test?

Type: instancemethod Base Class: <type 'instancemethod'> String Form: <bound method NoseTester.test of <scipy.testing.nosetester.NoseTester object at 0x1b 2d930>> Namespace: Interactive File: /Users/rkern/svn/scipy/scipy/testing/nosetester.py Definition: scipy.test(self, label='fast', verbose=1, extra_argv=None, doctests=False) Docstring: Run tests for module using nose

Parameters ---------- label : {'fast', 'full', '', attribute identifer} Identifies test to run. This can be a string to pass to the nosetests executable with the'-A' option, or one of several special values. Special values are: 'fast' - the default - which corresponds to nosetests -A option of 'not slow'. 'full' - fast (as above) and slow test as in no -A option to nosetests - same as '' None or '' - run all tests attribute_identifier - string passed directly to nosetests as '-A' verbose : integer verbosity value for test outputs, 1-10 extra_argv : list List with any extra args to pass to nosetests doctests : boolean If True, run doctests in module, default False

-- 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@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user

Joshua Lippai wrote:

Alright, I rebuilt scipy and managed to whittle it down to 7 errors instead of 8, but that failure is still there, and there weren't any alarms during the building other than:

AFAIK, the trunk of scipy does have some errors for some time; I am not involved in the changes, but from my own understanding, it looks like some big changes were done in some parts of scipy (nd_image, sparse). I don't have errors outside those modules. I would not worry too much about those errors before the code stabilize in those modules (of course, if you use those modules, that's another story). cheers, David

That's a relief to know, and it lets me know of something that I could even try working on! That covers the errors, but what of the failure of test_namespace? It looks like the 'X' array is coming out exactly twice the 'Y' array. Is this a known problem as well? Josh On Sat, Mar 22, 2008 at 2:39 AM, Nils Wagner <nwagner@iam.uni-stuttgart.de> wrote:

On Sat, 22 Mar 2008 17:41:45 +0900 David Cournapeau <david@ar.media.kyoto-u.ac.jp> wrote:

...

Joshua Lippai wrote:

...

Alright, I rebuilt scipy and managed to whittle it down to 7 errors instead of 8, but that failure is still there, and there weren't any alarms during the building other than:

AFAIK, the trunk of scipy does have some errors for some time; I am not involved in the changes, but from my own understanding, it looks like some big changes were done in some parts of scipy (nd_image, sparse). I don't have errors outside those modules. I would not worry too much about those errors before the code stabilize in those modules (of course, if you use those modules, that's another story).

cheers,

David

I have filed tickets for those errors

http://projects.scipy.org/scipy/scipy/ticket/586 http://projects.scipy.org/scipy/scipy/ticket/587

Nils

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