[SciPy-user] OS X test issues

Vincent Nijs v-nijs at kellogg.northwestern.edu
Thu Jan 18 21:19:58 CST 2007


I used steps 1,2, and 4 on a G4 laptop (OS X 10.4.8). Installed fftw using
MacPorts.

I get the same check_dot errors as Srinath but not the scipy.io ones. I do
also get the following check_normal and check loadmat errors:

======================================================================
FAIL: check_normal (scipy.stats.tests.test_morestats.test_anderson)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/scipy/stats/tests/test_morestats.py", line 45, in check_normal
    assert_array_less(crit[:-1], A)
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/numpy/testing/utils.py", line 235, in assert_array_less
    header='Arrays are not less-ordered')
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/numpy/testing/utils.py", line 215, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not less-ordered

(mismatch 100.0%)
 x: array([ 0.538,  0.613,  0.736,  0.858])
 y: array(nan)

======================================================================
FAIL: check loadmat case sparse
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/scipy/io/tests/test_mio.py", line 85, in cc
    self._check_case(name, files, expected)
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/scipy/io/tests/test_mio.py", line 80, in _check_case
    self._check_level(k_label, expected, matdict[k])
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/scipy/io/tests/test_mio.py", line 63, in _check_level
    decimal = 5)
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/numpy/testing/utils.py", line 230, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File 
"/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packag
es/numpy/testing/utils.py", line 215, in assert_array_compare
    assert cond, msg
AssertionError: 
Arrays are not almost equal
test sparse; file 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package
s/scipy/io/tests/./data/testsparse_6.5.1_GLNX86.mat, variable testsparse
(mismatch 46.6666666667%)
 x: array([[  3.03865194e-319,   3.16202013e-322,   1.04346664e-320,
          2.05531309e-320,   2.56123631e-320],
       [  3.16202013e-322,   0.00000000e+000,   0.00000000e+000,...
 y: array([[ 1.,  2.,  3.,  4.,  5.],
       [ 2.,  0.,  0.,  0.,  0.],
       [ 3.,  0.,  0.,  0.,  0.]])


Ran 1604 tests in 27.705s

FAILED (failures=4)





On 1/18/07 8:13 PM, "Srinath Vadlamani" <srinath at txcorp.com> wrote:

> I have made my n-th attempt at installing a proper scipy version on my
> MacBook Pro.  These are my steps.
> 1)svn co numpy and scipy
> 2)built numpy configured with gfortran
> 3)built fftw
> 4)built scipy configured with gfortran
> 
> All tests for numpy pass.
> For scipy its a different story:
> ============================
> Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import numpy
>>>> import scipy
>>>> scipy.test(1)
>   Found 4 tests for scipy.io.array_import
>   Found 128 tests for scipy.linalg.fblas
>   Found 397 tests for scipy.ndimage
>   Found 53 tests for scipy.linalg.decomp
>   Found 20 tests for scipy.fftpack.pseudo_diffs
>   Found 6 tests for scipy.optimize.optimize
>   Found 12 tests for scipy.io.mmio
>   Found 4 tests for scipy.linalg.lapack
>   Found 18 tests for scipy.fftpack.basic
>   Found 4 tests for scipy.io.recaster
>   Found 4 tests for scipy.optimize.zeros
> Warning: FAILURE importing tests for <module 'scipy.io.mio' from
> '...site-packages/scipy/io/mio.pyc'>
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/
> scipy/sparse/sparse.py:15:
> Import
> Error: Failure linking new module:
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package
> s/scipy/sparse/sparsetools.so: Library not loaded:
> /usr/local/lib/libgfortran.1.dylib
>   Referenced from:
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/
> scipy/sparse/s
> parsetools.so
>   Reason: image not found (in ?)
> 
> ****************************************************************
> 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.
> ****************************************************************
> 
>   Found 42 tests for scipy.lib.lapack
>   Found 128 tests for scipy.lib.blas.fblas
>   Found 7 tests for scipy.linalg.matfuncs
>   Found 41 tests for scipy.linalg.basic
>   Found 1 tests for scipy.optimize.cobyla
>   Found 16 tests for scipy.lib.blas
>   Found 14 tests for scipy.linalg.blas
>   Found 4 tests for scipy.fftpack.helper
>   Found 0 tests for __main__
> 
> Don't worry about a warning regarding the number of bytes read.
> Warning: 1000000 bytes requested, 20 bytes read.
> ...E...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
> ..............................................................................
> .................................
> ..............................................................................
> .................................
> ..............................................................................
> .................................
> ..............................................................................
> .................................
> .............................................E..
> ****************************************************************
> 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.
> ****************************************************************
> 
> .........................................................................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
> ...Result may be inaccurate, approximate err = 2.66420674161e-08
> ...Result may be inaccurate, approximate err = 7.27595761418e-12
> .....................................................F.......
> ****************************************************************
> 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.
> ****************************************************************
> 
> .......F..........
> ======================================================================
> ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/io/tests/test_array
> _import.py", line 55, in check_integer
>     from scipy import stats
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/stats/__init__.py",
>  line 7, in ?
>     from stats import *
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/stats/stats.py",
> li
> ne 190, in ?
>     import scipy.special as special
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/special/__init__.py
> ", line 8, in ?
>     from basic import *
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/special/basic.py",
> 
> line 8, in ?
>     from _cephes import *
> ImportError: Failure linking new module:
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-p
> ackages/scipy/special/_cephes.so: Symbol not found: _e_wsle
>   Referenced from:
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/
> scipy/special/
> _cephes.so
>   Expected in: dynamic lookup
> 
> 
> ======================================================================
> ERROR: check_simple_todense (scipy.io.tests.test_mmio.test_mmio_coordinate)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/io/tests/test_mmio.
> py", line 151, in check_simple_todense
>     b = mmread(fn).todense()
> AttributeError: 'numpy.ndarray' object has no attribute 'todense'
> 
> ======================================================================
> FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/lib/blas/tests/test
> _blas.py", line 76, in check_dot
>     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /numpy/testing/utils.py",
> 
> line 156, in assert_almost_equal
>     assert round(abs(desired - actual),decimal) == 0, msg
> AssertionError:
> Items are not equal:
>  ACTUAL: 9.8394918217557107e-39j
>  DESIRED: (-9+2j)
> 
> ======================================================================
> FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /scipy/linalg/tests/test_b
> las.py", line 75, in check_dot
>     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages
> /numpy/testing/utils.py",
> 
> line 156, in assert_almost_equal
>     assert round(abs(desired - actual),decimal) == 0, msg
> AssertionError:
> Items are not equal:
>  ACTUAL: 9.7746285184390436e-39j
>  DESIRED: (-9+2j)
> 
> ----------------------------------------------------------------------
> Ran 903 tests in 1.773s
> 
> FAILED (failures=2, errors=2)
> <unittest.TextTestRunner object at 0x360ea10>
>>>> 
> =====================================
> Any suggestions will help.
> 
> thanks,
> SV

-- 
Vincent R. Nijs
Assistant Professor of Marketing
Kellogg School of Management, Northwestern University
2001 Sheridan Road, Evanston, IL 60208-2001
Phone: +1-847-491-4574 Fax: +1-847-491-2498
E-mail: v-nijs at kellogg.northwestern.edu
Skype: vincentnijs





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