[Numpy-discussion] recompiling needed for binary module after numpy 1.0

belinda thom bthom at cs.hmc.edu
Mon Jan 8 23:34:08 CST 2007


Thanks for the Intel update.

I'm doing the same for my PPC (Powerbook, G4, OS X 10.4.8), and have  
some failures in scipy's tests. Did you try doing:

 >>> import numpy as N
 >>> N.test()

and

 >>> import scipy as S
 >>> S.test()?

For me, the latter one fails (both install and S.test() I/O appended).

> I just got a new MacBook Pro, core 2 duo.  There is no
> numpy/scipy fink distro for the intels yet so I tried out
> Robert's suggestions above.  I installed python 2.5 as
> the base.  I can confirm that all is working well for
> numpy and scipy.
>
> Matplotlib compiled, but gave some odd warnings such
> as
>

Perhaps I should attempt to install matplot lib at this point---I  
don't know. Any idea if the FAILUREs I'm seeing are a problem?

Thx,

--b

Below, I paste the output from python setup.py install (for scipy) as  
well as the command I ran inside of python to check scipy's  
functionality.

bthom at tweedledee.local [5:51pm] ~/Download/scipy-0.5.2
4 % sudo python setup.py install
Password:
mkl_info:
   libraries mkl,vml,guide not found in /Library/Frameworks/ 
Python.framework/Versions/2.4/lib
   libraries mkl,vml,guide not found in /usr/local/lib
   libraries mkl,vml,guide not found in /usr/lib
   libraries mkl,vml,guide not found in /opt/local/lib
   NOT AVAILABLE

fftw3_info:
   libraries fftw3 not found in /Library/Frameworks/Python.framework/ 
Versions/2.4/lib
   libraries fftw3 not found in /usr/local/lib
   libraries fftw3 not found in /usr/lib
   libraries fftw3 not found in /opt/local/lib
   fftw3 not found
   NOT AVAILABLE

fftw2_info:
   libraries rfftw,fftw not found in /Library/Frameworks/ 
Python.framework/Versions/2.4/lib
   libraries rfftw,fftw not found in /usr/local/lib
   libraries rfftw,fftw not found in /usr/lib
   libraries rfftw,fftw not found in /opt/local/lib
   fftw2 not found
   NOT AVAILABLE

dfftw_info:
   libraries drfftw,dfftw not found in /Library/Frameworks/ 
Python.framework/Versions/2.4/lib
   libraries drfftw,dfftw not found in /usr/local/lib
   libraries drfftw,dfftw not found in /usr/lib
   libraries drfftw,dfftw not found in /opt/local/lib
   dfftw not found
   NOT AVAILABLE

djbfft_info:
   NOT AVAILABLE

blas_opt_info:
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/ 
vecLib.framework/Headers']

lapack_opt_info:
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-faltivec']

non-existing path in 'Lib/linsolve': 'tests'
umfpack_info:
   libraries umfpack not found in /Library/Frameworks/ 
Python.framework/Versions/2.4/lib
   libraries umfpack not found in /usr/local/lib
   libraries umfpack not found in /usr/lib
   libraries umfpack not found in /opt/local/lib
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/numpy/distutils/system_info.py:401: UserWarning:
     UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/ 
umfpack/)
     not found. Directories to search for the libraries can be  
specified in the
     numpy/distutils/site.cfg file (section [umfpack]) or by setting
     the UMFPACK environment variable.
   warnings.warn(self.notfounderror.__doc__)
   NOT AVAILABLE

non-existing path in 'Lib/maxentropy': 'doc'
Warning: Subpackage 'Lib' configuration returned as 'scipy'
running install
running build
running config_fc
running build_src
building py_modules sources
building library "dfftpack" sources
building library "linpack_lite" sources
<snip>
building library "specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
<snip>
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
building extension "scipy.stats.futil" sources
f2py options: []
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
   adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources.
   adding 'build/src.macosx-10.3-fat-2.4' to include_dirs.
   adding 'build/src.macosx-10.3-fat-2.4/Lib/stats/mvn- 
f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building data_files sources
running build_py
copying build/src.macosx-10.3-fat-2.4/scipy/__config__.py -> build/ 
lib.macosx-10.3-fat-2.4/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize NAGFCompiler
customize AbsoftFCompiler
customize IbmFCompiler
Could not locate executable g77
Could not locate executable f77
Could not locate executable f95
customize GnuFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
customize AbsoftFCompiler
customize IbmFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
running install_lib
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy
<snip>
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/lib/blas
copying build/lib.macosx-10.3-fat-2.4/scipy/lib/blas/__init__.py -> / 
Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/lib/blas
copying build/lib.macosx-10.3-fat-2.4/scipy/lib/blas/cblas.so -> / 
Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/lib/blas
<snip>
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/weave
copying build/lib.macosx-10.3-fat-2.4/scipy/weave/wx_spec.py -> / 
Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/weave
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/__config__.py to __config__.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/__init__.py to __init__.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/__svn_version__.py to
<snip>
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/slice_handler.py to  
slice_handler.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/standard_array_spec.py to  
standard_array_spec.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/swig2_spec.py to swig2_spec.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/swigptr.py to swigptr.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/swigptr2.py to swigptr2.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/vtk_spec.py to vtk_spec.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/weave_version.py to  
weave_version.pyc
byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/wx_spec.py to wx_spec.pyc
running install_data
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/sparse/tests
copying Lib/sparse/tests/test_sparse.orig -> /Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ 
sparse/tests/
<snip>
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/maxentropy/examples
copying Lib/maxentropy/examples/bergerexamplesimulated.py -> /Library/ 
Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ 
scipy/maxentropy/examples/
copying Lib/maxentropy/examples/conditionalexample1.py -> /Library/ 
Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ 
scipy/maxentropy/examples/
copying Lib/maxentropy/examples/conditionalexample2.py -> /Library/ 
Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ 
scipy/maxentropy/examples/
copying Lib/maxentropy/examples/bergerexample.py -> /Library/ 
Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ 
scipy/maxentropy/examples/
copying ./TOCHANGE.txt -> /Library/Frameworks/Python.framework/ 
Versions/2.4/lib/python2.4/site-packages/scipy
copying ./DEVELOPERS.txt -> /Library/Frameworks/Python.framework/ 
Versions/2.4/lib/python2.4/site-packages/scipy
copying ./THANKS.txt -> /Library/Frameworks/Python.framework/Versions/ 
2.4/lib/python2.4/site-packages/scipy
copying ./LICENSE.txt -> /Library/Frameworks/Python.framework/ 
Versions/2.4/lib/python2.4/site-packages/scipy
copying ./LATEST.txt -> /Library/Frameworks/Python.framework/Versions/ 
2.4/lib/python2.4/site-packages/scipy
copying ./FORMAT_GUIDELINES.txt -> /Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy
copying ./INSTALL.txt -> /Library/Frameworks/Python.framework/ 
Versions/2.4/lib/python2.4/site-packages/scipy
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/linalg/tests
copying Lib/linalg/tests/test_blas.py -> /Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ 
linalg/tests/
<snip>
site-packages/scipy/fftpack/tests/
creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/weave/doc
copying Lib/weave/doc/tutorial.html -> /Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/ 
doc/

bthom at tweedledee.local [5:52pm] ~/Download/scipy-0.5.2
5 % python
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 scipy as S
 >>> S.test()
   Found 4 tests for scipy.io.array_import
   Found 1 tests for scipy.cluster.vq
   Found 128 tests for scipy.linalg.fblas
<snip>
   Found 18 tests for scipy.fftpack.basic
   Found 4 tests for scipy.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack'  
from '.../linsolve/umfpack/__init__.pyc'>
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:  
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
   Found 4 tests for scipy.optimize.zeros
   Found 28 tests for scipy.io.mio
   Found 41 tests for scipy.linalg.basic
   Found 2 tests for scipy.maxentropy.maxentropy
   Found 358 tests for scipy.special.basic
   Found 128 tests for scipy.lib.blas.fblas
   Found 7 tests for scipy.linalg.matfuncs

****************************************************************
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
Warning: FAILURE importing tests for <module  
'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/ 
umfpack.pyc'>
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- 
packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17:  
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
   Found 1 tests for scipy.optimize.cobyla
   Found 16 tests for scipy.lib.blas
   Found 1 tests for scipy.integrate
   Found 14 tests for scipy.linalg.blas
   Found 4 tests for scipy.fftpack.helper
   Found 4 tests for scipy.signal.signaltools
   Found 0 tests for __main__

Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
<snip>
.....Use minimum degree ordering on A'+A.
....................................../Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ 
interpolate/fitpack2.py:457: UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
   warnings.warn(message)
........................................................................ 
........................Ties preclude use of exact statistic.
..Ties preclude use of exact statistic.
........
****************************************************************
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.
****************************************************************

.......................F................................................ 
............................................................
<snip>

...Result may be inaccurate, approximate err = 1.6582899877e-08
...Result may be inaccurate, approximate err = 4.54747350886e-13
......................................................F.......Residual:  
1.05006926991e-07
.
****************************************************************
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..............
======================================================================
FAIL: test_smallest_same_kind  
(scipy.io.tests.test_recaster.test_recaster)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_recaster.py", line 61, in  
test_smallest_same_kind
     assert C is not None, 'Got unexpected None from %s' % T
AssertionError: Got unexpected None from <type 'numpy.float128'>

======================================================================
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: (-1.9987130165100098+4.5784586609566519e-37j)
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_blas.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: (-1.9987130165100098+4.5784443116603772e-37j)
DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 1596 tests in 14.230s

FAILED (failures=3)
<unittest.TextTestRunner object at 0x2cf6bb0>
 >>>





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