[SciPy-user] umfpack and building scipy from source

Ryan Krauss ryanlists at gmail.com
Thu Nov 30 13:36:53 CST 2006


Following Robert Kern's advice I am getting very close.  The API error
is now gone.

There is my current scipy.test() output.

In [4]: scipy.test()
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' fr
om '...y\\linsolve\\umfpack\\umfpack.pyc'>
C:\Python24\Lib\site-packages\scipy\linsolve\umfpack\tests\test_umfpack.py:17: A
ttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 4 tests for scipy.io.array_import
  Found 2 tests for scipy.maxentropy.maxentropy
  Found 1 tests for scipy.cluster.vq
  Found 397 tests for scipy.ndimage
  Found 98 tests for scipy.stats.stats
  Found 53 tests for scipy.linalg.decomp
  Found 3 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 4 tests for scipy.signal.signaltools
  Found 128 tests for scipy.linalg.fblas
  Found 6 tests for scipy.interpolate.fitpack
  Found 6 tests for scipy.interpolate
  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.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '...\
\linsolve\\umfpack\\__init__.pyc'>
C:\Python24\Lib\site-packages\scipy\linsolve\umfpack\tests\test_umfpack.py:17: A
ttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 4 tests for scipy.optimize.zeros
  Found 28 tests for scipy.io.mio
  Found 4 tests for scipy.fftpack.helper
  Found 41 tests for scipy.linalg.basic
  Found 358 tests for scipy.special.basic
  Found 10 tests for scipy.integrate.quadpack
  Found 7 tests for scipy.linalg.matfuncs
  Found 1 tests for scipy.integrate
  Found 42 tests for scipy.lib.lapack
  Found 12 tests for scipy.io.mmio
  Found 1 tests for scipy.optimize.cobyla
  Found 128 tests for scipy.lib.blas.fblas
  Found 16 tests for scipy.lib.blas
  Found 14 tests for scipy.linalg.blas
  Found 70 tests for scipy.stats.distributions
  Found 0 tests for __main__

Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
................................................................................
................................................................................
................................................................................
................................................................................
................................................................................
................................................................................
...........................................................................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.
.............................................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
..c:\python24\lib\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.
...............................E................................................
................................................................................
................................................................................
................................................................................
................................................................................
..............................................................................Re
sult may be inaccurate, approximate err = 3.64830903151e-009
...Result may be inaccurate, approximate err = 1.39218513881e-010
...Residual: 1.05006950608e-007
...........................................................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
................................................................................
......................
======================================================================
ERROR: test_smallest_same_kind (scipy.io.tests.test_recaster.test_recaster)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python24\Lib\site-packages\scipy\io\tests\test_recaster.py", line 61,
 in test_smallest_same_kind
    assert C.dtype.type == req_type, \
AttributeError: 'NoneType' object has no attribute 'dtype'

----------------------------------------------------------------------
Ran 1595 tests in 3.344s

FAILED (errors=1)
Out[4]: <unittest.TextTestRunner object at 0x03EB48F0>

What else should I try?

Ryan

On 11/30/06, Robert Kern <robert.kern at gmail.com> wrote:
> Ryan Krauss wrote:
> > I may have had the misfortune of checking out of svn last night while
> > numpy and scipy were out of sync.  I re-did my svn checkout just now
> > and numpy didn't change, but scipy went from version 2339 to 2342.  I
> > now get fewer errors.  I also did a python setup.py clean for each
> > before rebuilding and deleted site-packages/numpy and /scipy before
> > rebuilding.
>
> Actually, this is probably the problem. Don't rely on "python setup.py clean" to
> do the right thing. distutils sometimes misses things. Just delete build/ entirely.
>
> --
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless enigma
>  that is made terrible by our own mad attempt to interpret it as though it had
>  an underlying truth."
>   -- Umberto Eco
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>


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