[SciPy-user] scipy super pack installer for win32: please test

Alan G Isaac aisaac@american....
Wed Oct 22 17:04:42 CDT 2008


>> http://www.ar.media.kyoto-u.ac.jp/members/david/archives/numpy/scipy-0.7.0.dev4826-win32-superpack-python2.5.exe 

joep wrote:
> when I run scipy.test() in a command shell, 
> or ipython shell, then I get a large output with Depreciation Warnings 
> and test output. 

Similar experience. Three failures. (I know these are not
a current concern.)  Output below.
Alan


Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310
32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys, scipy
>>> sys.stderr = open('c:/temp/temp.out','w')
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.2.0
NumPy is installed in C:\Python25\lib\site-packages\numpy
SciPy version 0.7.0.dev4826
SciPy is installed in C:\Python25\lib\site-packages\scipy
Python version 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 
bit (Int
el)]
nose version 0.10.1
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
ATLAS version 3.8.2 built by david on Tue Aug  5 13:01:25 TST 2008:
    UNAME    : CYGWIN_NT-5.1 donau-win 1.5.25(0.156/4/2) 2008-06-12 
19:34 i686 Cy
gwin
    INSTFLG  : -1 0 -a 1
    ARCHDEFS : -DATL_OS_WinNT -DATL_ARCH_P4 -DATL_CPUMHZ=3200 -DGCCWIN 
-DUseClock
  -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
    F2CDEFS  : -DAdd__ -DF77_INTEGER=int -DStringSunStyle
    CACHEEDGE: 3145728
    F77      : g77, version GNU Fortran (GCC) 3.4.4 (cygming special, 
gdc 0.12, u
sing dmd 0.125)
    F77FLAGS : -O -m32
    SMC      : gcc, version gcc (GCC) 3.4.4 (cygming special, gdc 0.12, 
using dmd
  0.125)
    SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -m32
    SKC      : gcc, version gcc (GCC) 3.4.4 (cygming special, gdc 0.12, 
using dmd
  0.125)
    SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -m32
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 = 9.82300567882e-009
Result may be inaccurate, approximate err = 1.87387729512e-010
warning: specified build_dir '_bad_path_' does not exist or is not 
writable. Try
ing default locations
warning: specified build_dir '_bad_path_' does not exist or is not 
writable. Try
ing default locations
error removing c:\docume~1\alanis~1\locals~1\temp\tmpkbpafhcat_test: 
c:\docume~1
\alanis~1\locals~1\temp\tmpkbpafhcat_test: The directory is not empty
building extensions here: c:\docume~1\alanis~1\locals~1\temp\Alan 
Isaac\python25
_compiled\m4
<nose.result.TextTestResult run=2317 errors=0 failures=3>
>>>


And here is the error log:

C:\Python25\lib\site-packages\scipy\linsolve\__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to
scipy.sparse.linalg.dsolve
   warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', 
DeprecationWarning)
.................................................................................................................................C:\Python25\lib\site-packages\scipy\cluster\vq.py:570: 
UserWarning: One of the clusters is empty. Re-run kmean with a different 
initialization.
   warnings.warn("One of the clusters is empty. "
...................................................C:\Python25\lib\site-packages\scipy\integrate\odepack.py:144: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   ixpr, mxstep, mxhnil, mxordn, mxords)
C:\Python25\lib\site-packages\scipy\integrate\odepack.py:144: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   ixpr, mxstep, mxhnil, mxordn, mxords)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:304: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qawse(func,a,b,wvar,integr,args,full_output,epsabs,epsrel,limit)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:304: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qawse(func,a,b,wvar,integr,args,full_output,epsabs,epsrel,limit)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:306: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qawce(func,a,b,wvar,args,full_output,epsabs,epsrel,limit)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:306: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qawce(func,a,b,wvar,args,full_output,epsabs,epsrel,limit)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:295: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qawfe(thefunc,-b,wvar,integr,args,full_output,epsabs,limlst,limit,maxp1)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:295: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qawfe(thefunc,-b,wvar,integr,args,full_output,epsabs,limlst,limit,maxp1)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:249: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return _quadpack._qagse(func,a,b,args,full_output,epsabs,epsrel,limit)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:249: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return _quadpack._qagse(func,a,b,args,full_output,epsabs,epsrel,limit)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:251: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:251: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:273: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qawoe(func,a,b,wvar,integr,args,full_output,epsabs,epsrel,limit,maxp1,1)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:273: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qawoe(func,a,b,wvar,integr,args,full_output,epsabs,epsrel,limit,maxp1,1)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:280: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qawfe(func,a,wvar,integr,args,full_output,epsabs,limlst,limit,maxp1)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:280: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qawfe(func,a,wvar,integr,args,full_output,epsabs,limlst,limit,maxp1)
.C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:259: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   return 
_quadpack._qagpe(func,a,b,the_points,args,full_output,epsabs,epsrel,limit)
C:\Python25\lib\site-packages\scipy\integrate\quadpack.py:259: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   return 
_quadpack._qagpe(func,a,b,the_points,args,full_output,epsabs,epsrel,limit)
......C:\Python25\lib\site-packages\scipy\interpolate\fitpack2.py:479: 
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)
....C:\Python25\lib\site-packages\scipy\interpolate\fitpack2.py:420: 
UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
   warnings.warn(message)
...........C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:760: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   tx,ty,nxest,nyest,wrk,lwrk1,lwrk2)
C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:760: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   tx,ty,nxest,nyest,wrk,lwrk1,lwrk2)
C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:837: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   z,ier=_fitpack._bispev(tx,ty,c,kx,ky,x,y,dx,dy)
C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:837: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   z,ier=_fitpack._bispev(tx,ty,c,kx,ky,x,y,dx,dy)
...............................C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:485: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   y,ier=_fitpack._spl_(x,der,t,c,k)
C:\Python25\lib\site-packages\scipy\interpolate\fitpack.py:485: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   y,ier=_fitpack._spl_(x,der,t,c,k)
..................KK..C:\Python25\lib\site-packages\scipy\io\tests\test_array_import.py:29: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   b = numpyio.fread(fid,1000000,N.Int16,N.Int)
C:\Python25\lib\site-packages\scipy\io\tests\test_array_import.py:29: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   b = numpyio.fread(fid,1000000,N.Int16,N.Int)
.C:\Python25\lib\site-packages\numpy\lib\utils.py:106: 
DeprecationWarning: write_array is deprecated
   warnings.warn(str1, DeprecationWarning)
C:\Python25\lib\site-packages\numpy\lib\utils.py:106: 
DeprecationWarning: read_array is deprecated
   warnings.warn(str1, DeprecationWarning)
......................C:\Python25\lib\site-packages\numpy\lib\utils.py:106: 
DeprecationWarning: npfile is deprecated
   warnings.warn(str1, DeprecationWarning)
....................................................................................................................................................................................FF................................................................................................................................................................................................................................................................................................F...........................................................................................................................................................................................................................................................................................................................................................................................................C:\Python25\lib\site-packages\scipy\odr\odrpack.py:1055: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   self.output = Output(apply(odr, args, kwds))
C:\Python25\lib\site-packages\scipy\odr\odrpack.py:1055: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   self.output = Output(apply(odr, args, kwds))
.................C:\Python25\lib\site-packages\scipy\optimize\minpack.py:270: 
DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
   retval = 
_minpack._lmdif(func,x0,args,full_output,ftol,xtol,gtol,maxfev,epsfcn,factor,diag)
C:\Python25\lib\site-packages\scipy\optimize\minpack.py:270: 
DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use 
PyArray_NewFromDescr.
   retval = 
_minpack._lmdif(func,x0,args,full_output,ftol,xtol,gtol,maxfev,epsfcn,factor,diag)
.................................SSSSSSSSSSS...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................C:\Python25\lib\site-packages\scipy\stats\stats.py:413: 
DeprecationWarning: scipy.stats.mean is deprecated; please update your 
code to use numpy.mean.
Please note that:
     - numpy.mean axis argument defaults to None, not 0
     - numpy.mean has a ddof argument to replace bias in a more general 
manner.
       scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
axis=0, ddof=1).
   axis=0, ddof=1).""", DeprecationWarning)
.C:\Python25\lib\site-packages\scipy\stats\stats.py:1237: 
DeprecationWarning: scipy.stats.std is deprecated; please update your 
code to use numpy.std.
Please note that:
     - numpy.std axis argument defaults to None, not 0
     - numpy.std has a ddof argument to replace bias in a more general 
manner.
       scipy.stats.std(a, bias=True) can be replaced by numpy.std(x,
axis=0, ddof=1).
   axis=0, ddof=1).""", DeprecationWarning)
C:\Python25\lib\site-packages\scipy\stats\stats.py:1214: 
DeprecationWarning: scipy.stats.var is deprecated; please update your 
code to use numpy.var.
Please note that:
     - numpy.var axis argument defaults to None, not 0
     - numpy.var has a ddof argument to replace bias in a more general 
manner.
       scipy.stats.var(a, bias=True) can be replaced by numpy.var(x,
axis=0, ddof=1).
   axis=0, ddof=1).""", DeprecationWarning)
.C:\Python25\lib\site-packages\scipy\stats\morestats.py:618: 
UserWarning: Ties preclude use of exact statistic.
   warnings.warn("Ties preclude use of exact statistic.")
......C:\Python25\lib\site-packages\scipy\stats\stats.py:491: 
DeprecationWarning: scipy.stats.median is deprecated; please update your 
code to use numpy.median.
Please note that:
     - numpy.median axis argument defaults to None, not 0
     - numpy.median has a ddof argument to replace bias in a more 
general manner.
       scipy.stats.median(a, bias=True) can be replaced by numpy.median(x,
axis=0, ddof=1).
   axis=0, ddof=1).""", DeprecationWarning)
......................................................C:\Python25\lib\site-packages\numpy\lib\function_base.py:343: 
Warning:
             The semantics of histogram has been modified in
             the current release to fix long-standing issues with
             outliers handling. The main changes concern
             1. the definition of the bin edges,
                now including the rightmost edge, and
             2. the handling of upper outliers, now ignored rather
                than tallied in the rightmost bin.
             The previous behaviour is still accessible using
             `new=False`, but is scheduled to be deprecated in the
             next release (1.3).

             *This warning will not printed in the 1.3 release.*

             Use `new=True` to bypass this warning.

             Please read the docstring for more information.

   """, Warning)
....................................................................................................................................................................................................................................
======================================================================
FAIL: test_lapack.test_all_lapack
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\lib\site-packages\nose\case.py", line 203, in runTest
     self.test(*self.arg)
   File 
"C:\Python25\Lib\site-packages\scipy\lib\lapack\tests\esv_tests.py", 
line 41, in check_syevr
     assert_array_almost_equal(w,exact_w)
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
311, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
296, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
  x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
  y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: test_lapack.test_all_lapack
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\lib\site-packages\nose\case.py", line 203, in runTest
     self.test(*self.arg)
   File 
"C:\Python25\Lib\site-packages\scipy\lib\lapack\tests\esv_tests.py", 
line 66, in check_syevr_irange
     assert_array_almost_equal(w,exact_w[rslice])
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
311, in assert_array_almost_equal
     header='Arrays are not almost equal')
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
296, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
  x: array([-0.66992444,  0.48769444,  9.18222618], dtype=float32)
  y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: test_imresize (test_pilutil.TestPILUtil)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 82, in skipper
     return f(*args, **kwargs)
   File 
"C:\Python25\Lib\site-packages\scipy\misc\tests\test_pilutil.py", line 
24, in test_imresize
     assert_equal(im1.shape,(11,22))
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
174, in assert_equal
     assert_equal(len(actual),len(desired),err_msg,verbose)
   File "C:\Python25\Lib\site-packages\numpy\testing\utils.py", line 
183, in assert_equal
     raise AssertionError(msg)
AssertionError:
Items are not equal:
  ACTUAL: 0
  DESIRED: 2

======================================================================
KNOWNFAIL: test_mio.test_load
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\lib\site-packages\nose\case.py", line 203, in runTest
     self.test(*self.arg)
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 119, in skipper
     raise KnownFailureTest, msg
KnownFailureTest: Test skipped due to known failure

======================================================================
KNOWNFAIL: test_mio.test_round_trip
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\lib\site-packages\nose\case.py", line 203, in runTest
     self.test(*self.arg)
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 119, in skipper
     raise KnownFailureTest, msg
KnownFailureTest: Test skipped due to known failure

======================================================================
SKIP: Getting factors of complex matrix
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Getting factors of real matrix
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Getting factors of complex matrix
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Getting factors of real matrix
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Prefactorize (with UMFPACK) matrix for solving with multiple rhs
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Prefactorize matrix for solving with multiple rhs
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Solve with UMFPACK: double precision complex
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Solve: single precision complex
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Solve with UMFPACK: double precision, sparse rhs
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Solve with UMFPACK: double precision
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

======================================================================
SKIP: Solve: single precision
----------------------------------------------------------------------
Traceback (most recent call last):
   File "C:\Python25\Lib\site-packages\numpy\testing\decorators.py", 
line 80, in skipper
     raise nose.SkipTest, msg
SkipTest: UMFPACK appears not to be compiled

----------------------------------------------------------------------
Ran 2317 tests in 70.461s

FAILED (failures=3)
























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