New to Scipy. I’ve installed scipy and numpy, but ween I run the scipy.test()

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Asked: June 4, 20262026-06-04T17:54:07+00:00 2026-06-04T17:54:07+00:00

New to Scipy. I’ve installed scipy and numpy, but ween I run the scipy.test()

0

New to Scipy.

I’ve installed scipy and numpy, but ween I run the scipy.test() I get many test fails.
I tried to find some common reasons and I have found several:

>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.6.2
NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
SciPy version 0.10.1
SciPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
Python version 2.7.3 (default, Apr 19 2012, 00:55:09) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
nose version 1.1.2
...

AssertionError:
Arrays are not almost equal to 7 decimals
...
AssertionError:
Not equal to tolerance rtol=1e-10, atol=1e-305
...
AssertionError: 
Arrays are not almost equal to 4 decimals
...
AssertionError: 
Max |adiff|: 92783.6
Max |rdiff|: 0.353942

Sounds to me like MPI problem or something, but I would’t really know.

Any help would be greatly appreciated.

Best, Jonathan.

——– EDIT ———
Tried it with scipy.test(verbose=10).
Most tests seems to work fine.
The fails starts with an ERROR. this is what I get:

   ERROR: Failure: DeprecationWarning (
The scipy.maxentropy module is deprecated in scipy 0.10, and scheduled to be
removed in 0.11.

If you are using some of the functionality in this module and are of the
opinion that it should be kept or moved somewhere - or you are even interested
to maintain/improve this whole module - please ask on the scipy-dev mailing
list.

The logsumexp function has already been moved to scipy.misc.)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/maxentropy/__init__.py", line 19, in <module>
    DeprecationWarning)
DeprecationWarning: 
The scipy.maxentropy module is deprecated in scipy 0.10, and scheduled to be
removed in 0.11.

If you are using some of the functionality in this module and are of the
opinion that it should be kept or moved somewhere - or you are even interested
to maintain/improve this whole module - please ask on the scipy-dev mailing
list.

The logsumexp function has already been moved to scipy.misc.

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 67, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 78, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_basic.TestNorm.test_overflow
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 581, in test_overflow
    assert_almost_equal(norm(a), a)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 451, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 846, in assert_array_almost_equal
    header=('Arrays are not almost equal to %d decimals' % decimal))
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 677, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals

(mismatch 100.0%)
 x: array(-0.0)
 y: array([  1.00000002e+20], dtype=float32)

======================================================================
FAIL: test_basic.TestNorm.test_stable
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 586, in test_stable
    assert_almost_equal(norm(a) - 1e4, 0.5)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: -10000.0
 DESIRED: 0.5

======================================================================
FAIL: test_basic.TestNorm.test_types
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 568, in test_types
    assert_allclose(norm(x), np.sqrt(14), rtol=tol)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 1213, in assert_allclose
    verbose=verbose, header=header)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 677, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=2.38419e-06, atol=0

(mismatch 100.0%)
 x: array(1.0842021724855044e-19)
 y: array(3.7416573867739413)

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 99, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 109, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 127, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/Library/Python/2.7/site-packages/numpy/testing/utils.py", line 467, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

----------------------------------------------------------------------
Ran 5101 tests in 56.140s


FAILED (KNOWNFAIL=12, SKIP=42, errors=1, failures=9)
<nose.result.TextTestResult run=5101 errors=1 failures=9>

I am really sorry to say I have no idea what the errors mean.

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1 Answer

Editorial Team · Answer 1 · 2026-06-04T17:54:09+00:00

The Scipy failures seem typical of what comes out from using a wrong (= ABI incompatibility with Veclib) Fortran compiler on OSX. The Numpy failures are pretty likely unrelated to these — difficult to say without seeing them.

The mess with binary interface incompatibilities and Fortran compilers on OSX is unfortunate and applies to all Fortran code, but not very easily fixable by Scipy developers — except that if an incorrect Fortran compiler is detected, the build should be made to fail with an informative error message…

You may find these useful: http://projects.scipy.org/scipy/ticket/1476 http://projects.scipy.org/scipy/ticket/1496

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