[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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