[Numpy-discussion] Error building numpy from svn, 2nd attempt

John Carter jnc at ecs.soton.ac.uk
Tue Jul 4 04:18:53 CDT 2006


Hi,

As is the way posting to a news group stirs the brain cell into 
activity and the problem is solved. or rather shifted.

I've downloaded the candidate version of mingw32 and using that to 
build numpy/scipy works, or rather it builds the extensions for Python 2.3

I believe that there are still problems as both numpy and scipy fail 
their tests. I'm also dubious as to whether they are finding Altas and Lapack.

Configuration:

Windows XP SP2
Cygwin = gcc version 3.4.4 (cygming special) (gdc 0.12, using dmd 0.125)
MinGW = gcc version 3.4.5 (mingw special)
Python = Python 2.3.3 (#51, Dec 18 2003, 20:22:39) [MSC v.1200 32 bit 
(Intel)] on win32

scipy, numpy, Atlas, Lapack all downloaded within the last 2 days


I've cut and pasted the error messages from the tests below.

Any help gratefully received.

John


=====
numpy
=====
D:.\numerical> python
Python 2.3.3 (#51, Dec 18 2003, 20:22:39) [MSC v.1200 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> numpy.test()
   Found 5 tests for numpy.distutils.misc_util
   Found 3 tests for numpy.lib.getlimits
   Found 30 tests for numpy.core.numerictypes
   Found 13 tests for numpy.core.umath
   Found 3 tests for numpy.core.scalarmath
   Found 8 tests for numpy.lib.arraysetops
   Found 42 tests for numpy.lib.type_check
   Found 101 tests for numpy.core.multiarray
   Found 36 tests for numpy.core.ma
   Found 10 tests for numpy.lib.twodim_base
   Found 10 tests for numpy.core.defmatrix
   Found 1 tests for numpy.lib.ufunclike
   Found 38 tests for numpy.lib.function_base
   Found 3 tests for numpy.dft.helper
   Found 1 tests for numpy.lib.polynomial
   Found 7 tests for numpy.core.records
   Found 26 tests for numpy.core.numeric
   Found 4 tests for numpy.lib.index_tricks
   Found 46 tests for numpy.lib.shape_base
   Found 0 tests for __main__
........................................................................................................
........................................................................................................
.........E..............................................................................................
...........................
======================================================================
ERROR: check_simple (numpy.lib.tests.test_twodim_base.test_histogram2d)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"C:\Python23\Lib\site-packages\numpy\lib\tests\test_twodim_base.py", 
line 137, in check_simple
     np.random.seed(1)
   File "mtrand.pyx", line 311, in mtrand.RandomState.seed
SystemError: C:\sf\python\dist\src-maint23\Objects\longobject.c:240: 
bad argument to internal function

----------------------------------------------------------------------
Ran 387 tests in 1.391s

FAILED (errors=1)
<unittest.TextTestRunner object at 0x010DB8F0>
 >>>

=====
scipy
=====
D:.\numerical> python
Python 2.3.3 (#51, Dec 18 2003, 20:22:39) [MSC v.1200 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
 >>> import scipy
 >>> scipy.test()
Overwriting lib=<module 'scipy.lib' from 
'C:\PYTHON23\lib\site-packages\scipy\lib\__init__.pyc'> from C:\PYTHON23\lib\si
te-packages\scipy\lib\__init__.pyc (was <module 'numpy.lib' from 
'C:\PYTHON23\lib\site-packages\numpy\lib\__init__.pyc'>
  from C:\PYTHON23\lib\site-packages\numpy\lib\__init__.pyc)
Overwriting fft=<function fft at 0x013E7AB0> from scipy.fftpack.basic 
(was <function fft at 0x00AAEE30> from numpy.dft.f
ftpack)
Overwriting ifft=<function ifft at 0x013E7AF0> from 
scipy.fftpack.basic (was <function ifft at 0x00AAEE70> from numpy.df
t.fftpack)
   Found 4 tests for scipy.io.array_import
   Found 128 tests for scipy.linalg.fblas
   Found 397 tests for scipy.ndimage
   Found 10 tests for scipy.integrate.quadpack
   Found 97 tests for scipy.stats.stats
   Found 47 tests for scipy.linalg.decomp
   Found 2 tests for scipy.integrate.quadrature
   Found 95 tests for scipy.sparse.sparse
   Found 20 tests for scipy.fftpack.pseudo_diffs
   Found 6 tests for scipy.optimize.optimize
   Found 5 tests for scipy.interpolate.fitpack
   Found 1 tests for scipy.interpolate
   Found 12 tests for scipy.io.mmio
   Found 10 tests for scipy.stats.morestats
   Found 4 tests for scipy.linalg.lapack
   Found 18 tests for scipy.fftpack.basic
   Found 4 tests for scipy.linsolve.umfpack
   Found 4 tests for scipy.optimize.zeros
   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
   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 70 tests for scipy.stats.distributions
   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.
.......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
........................................................................................................................
........................................................................................................................
........................................................................................................................
........................................................................................................................
.........................................................................Took 
13 points.
..........Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
........................Use minimum degree ordering on A'+A.
...................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
.................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
......................................C:\PYTHON23\lib\site-packages\scipy\interpolate\fitpack2.py:410: 
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.
****************************************************************

....................data-ftype: z compared to data D
Calling _superlu.zgssv
Use minimum degree ordering on A'+A.
.data-ftype: c compared to data F
Calling _superlu.cgssv
Use minimum degree ordering on A'+A.
.data-ftype: d compared to data d
Calling _superlu.dgssv
Use minimum degree ordering on A'+A.
.data-ftype: s compared to data f
Calling _superlu.sgssv
Use minimum degree ordering on A'+A.
........................................................................................................................
........................................................................................................................
....................................Gegenbauer, a =  2.7337413228
........................................................................................................................
.............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 = 4.1928136851e-009
...Result may be inaccurate, approximate err = 7.27595761418e-012
.............................................F................Residual: 
1.05006950319e-007
.
****************************************************************
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.
****************************************************************

............................................................................................
======================================================================
FAIL: check_simple (scipy.optimize.tests.test_cobyla.test_cobyla)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"C:\Python23\Lib\site-packages\scipy\optimize\tests\test_cobyla.py", 
line 20, in check_simple
     assert_almost_equal(x, [x0, x1], decimal=5)
   File "C:\Python23\Lib\site-packages\numpy\testing\utils.py", line 
152, in assert_almost_equal
     return assert_array_almost_equal(actual, desired, decimal, err_msg)
   File "C:\Python23\Lib\site-packages\numpy\testing\utils.py", line 
222, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "C:\Python23\Lib\site-packages\numpy\testing\utils.py", line 
207, in assert_array_compare
     assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
  x: array([ 4.957975  ,  0.64690335])
  y: array([ 4.95535625,  0.66666667])

----------------------------------------------------------------------
Ran 1552 tests in 5.828s

FAILED (failures=1)
<unittest.TextTestRunner object at 0x02671210>
 >>>





Dr. John N. Carter.                                        E-Mail : 
jnc at ecs.soton.ac.uk
Building 1, Room 
2005                                   http://www.ecs.soton.ac.uk/~jnc/
Information: Signals, Images, Systems            Phone  : +44 (0) 23 8059 2405
School of Electronics & Computer Science,     Fax      : +44 (0) 23 8059 4498
Southampton University, Hants, UK SO17 1BJ.





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