[MacPorts] #31084: py26-scipy failures on Lion

MacPorts noreply at macports.org
Sat Sep 3 16:00:56 PDT 2011


#31084: py26-scipy failures on Lion
--------------------------------------+-------------------------------------
 Reporter:  howarth@…                 |       Owner:  jmr@…           
     Type:  defect                    |      Status:  new             
 Priority:  Normal                    |   Milestone:                  
Component:  ports                     |     Version:  2.0.2           
 Keywords:                            |        Port:  py26-scipy      
--------------------------------------+-------------------------------------
Changes (by ryandesign@…):

  * owner:  macports-tickets@… => jmr@…
  * keywords:  python =>
 * cc: jmr, ram (removed)
 * cc: ram@… (added)


Old description:

> 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.

New description:

 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.

--

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Ticket URL: <https://trac.macports.org/ticket/31084#comment:2>
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