[SciPy-user] OS X test issues

Srinath Vadlamani srinath at txcorp.com
Thu Jan 18 20:13:13 CST 2007


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

-- 
==========================================================
Srinath Vadlamani			srinath at txcorp.com
Tech-X Corp.				o:303-996-2034
5621 Arapahoe Ave. Suite A		f:303-448-7756
Boulder, CO 80303			
==========================================================



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