py26-scipy failures on Lion

[howarth@…]

The py26-scipy package (and other python variants) show new failures on Lion...

[MacPro-3:~] howarth% python2.6
Python 2.6.7 (r267:88850, Aug 26 2011, 21:02:58) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
SciPy version 0.9.0
SciPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy
Python version 2.6.7 (r267:88850, Aug 26 2011, 21:02:58) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
nose version 1.0.0
.............................................................................................................................................................................................................K......................................................................................................................K..K.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS.....................................................F....FF.....S................................................................................................................................................................................................................K...........................................................................................................................................................................................SSSSS.........S.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:259: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
../opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:75: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
................K.K..KK.KK...........................................................................................................................................K...............................................................K...........................................................................................................................................................KK...............................................................................................................................................................................................................................................................................................................................................................................................................................K.K........................................................................................................................................................................................................................................................................................................................................................................................K........K.........SSSSSSS................................................................................................................................................................................................................................................................................................................................................................................................../opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py:3546: RuntimeWarning: overflow encountered in exp
  return exp(c*x-exp(x)-gamln(c))
................................./opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/distributions.py:3955: RuntimeWarning: invalid value encountered in sqrt
  vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
.........................................................................................................................................................................................................................................................................................................S..............................................................................................................................................................................................F.............................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, 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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, 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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/tests/test_blas.py", line 57, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, 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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/tests/test_blas.py", line 66, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, 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 "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/tests/test_blas.py", line 83, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_expon (test_morestats.TestAnderson)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/tests/test_morestats.py", line 72, in test_expon
    assert_array_less(crit[:-1], A)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 869, in assert_array_less
    header='Arrays are not less-ordered')
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 613, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='inf')
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py", line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not less-ordered

x and y inf location mismatch:
 x: array([ 0.911,  1.065,  1.325,  1.587])
 y: array(inf)

----------------------------------------------------------------------
Ran 4722 tests in 85.682s

FAILED (KNOWNFAIL=18, SKIP=31, failures=7)
<nose.result.TextTestResult run=4722 errors=0 failures=7>
>>> 

The issue and a fix is described in ​http://mail.scipy.org/pipermail/scipy-dev/2011-August/016467.html.

[howarth@…]

Portfile.diff to pass "-ff2c" on FFLAGS.

[howarth@…]

The same proposed fix from the attached Portfile.diff is required for the other python variants of scipy (py25-scipy, etc) in order to eliminate the test suite failures under Lion.

[ryandesign (Ryan Carsten Schmidt)]

Please remember to use WikiFormatting. Note that the Cc field requires complete email addresses.

[skymoo (Adam Mercer)]

I'm hoping to get round to unifying the py*-numpy and py*-scipy ports by this weekend so I will ensure this fix makes it into those, if I don't have the time I'll add this fix to the ports as they currently stand.

[skymoo (Adam Mercer)]

Hoping to get a unified port for scipy committed this weekend, once that had been committed I'll address this issue.

[skymoo (Adam Mercer)]

I still get these test failures after applying your patch with Xcode 4 on Snow Leopard

[skymoo (Adam Mercer)]

I don't get these failures after bumping to 0.10.0, are you still seeing them?

[skymoo (Adam Mercer)]

No response, assuming issue fixed. Reopen if this is still a problem.