[SciPy-user] scipy 0.6 installation problem

Yutec Sun dbm.sun@gmail....
Fri Nov 23 11:18:03 CST 2007


Hello,
I'd like to ask your favor for helping me install scipy 0.6.
I have a problem importing scipy. In fact, importing doesn't show an
error message, but scipy.test produces failures.
My OS is Ubuntu 7.10 (Gutsy Gibbon) amd64. Following the installation
instruction, I attach the messages for further information.
Please understand that I'm new to linux system and scipy, and let me
know how to successfully install scipy step by step.
I thank you for your help.

Best regards,

Yutec


--------------------------------------------------------------------------------------------------------------
1. Error message
--------------------------------------------------------------------------------------------------------------
yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy/distutils$ python
Python 2.5.1 (r251:54863, Oct  5 2007, 13:50:07)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test(level=1)
  Found 9/9 tests for scipy.cluster.vq
  Found 18/18 tests for scipy.fftpack.basic
  Found 4/4 tests for scipy.fftpack.helper
  Found 20/20 tests for scipy.fftpack.pseudo_diffs
  Found 1/1 tests for scipy.integrate
  Found 10/10 tests for scipy.integrate.quadpack
  Found 3/3 tests for scipy.integrate.quadrature
  Found 6/6 tests for scipy.interpolate
  Found 6/6 tests for scipy.interpolate.fitpack
  Found 4/4 tests for scipy.io.array_import
  Found 28/28 tests for scipy.io.mio
  Found 13/13 tests for scipy.io.mmio
  Found 5/5 tests for scipy.io.npfile
  Found 4/4 tests for scipy.io.recaster
  Found 16/16 tests for scipy.lib.blas
  Found 128/128 tests for scipy.lib.blas.fblas
  Found 42/42 tests for scipy.lib.lapack
  Found 41/41 tests for scipy.linalg.basic
<module 'scipy.linalg.fblas' from
'/usr/lib/python2.5/site-packages/scipy/linalg/fblas.so'>
  Found 16/16 tests for scipy.linalg.blas
  Found 72/72 tests for scipy.linalg.decomp
  Found 128/128 tests for scipy.linalg.fblas
  Found 6/6 tests for scipy.linalg.iterative
  Found 4/4 tests for scipy.linalg.lapack
  Found 7/7 tests for scipy.linalg.matfuncs
  Found 9/9 tests for scipy.linsolve.umfpack
  Found 2/2 tests for scipy.maxentropy
  Found 3/3 tests for scipy.misc.pilutil
  Found 399/399 tests for scipy.ndimage
  Found 5/5 tests for scipy.odr
  Found 8/8 tests for scipy.optimize
  Found 1/1 tests for scipy.optimize.cobyla
  Found 10/10 tests for scipy.optimize.nonlin
  Found 4/4 tests for scipy.optimize.zeros
  Found 5/5 tests for scipy.signal.signaltools
  Found 4/4 tests for scipy.signal.wavelets
  Found 152/152 tests for scipy.sparse
  Found 342/342 tests for scipy.special.basic
  Found 3/3 tests for scipy.special.spfun_stats
  Found 107/107 tests for scipy.stats
  Found 73/73 tests for scipy.stats.distributions
  Found 10/10 tests for scipy.stats.morestats
  Found 0/0 tests for __main__
/usr/lib/python2.5/site-packages/scipy/cluster/vq.py:477: UserWarning:
One of the clusters is empty. Re-run kmean with a different
initialization.
  warnings.warn("One of the clusters is empty. "
...exception raised as expected: One of the clusters is empty. Re-run
kmean with a different initialization.
................................................Residual: 1.05006987327e-07
..................../usr/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458:
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)
......
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
................................................................................................................................................................................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 = 1.56163357201e-08
...Result may be inaccurate, approximate err = 1.25221600096e-10
......Use minimum degree ordering on A'+A.
..Use minimum degree ordering on A'+A.
...Use minimum degree ordering on A'+A.
............................................................................................................./usr/lib/python2.5/site-packages/scipy/ndimage/interpolation.py:41:
UserWarning: Mode "reflect" may yield incorrect results on boundaries.
Please use "mirror" instead.
  warnings.warn('Mode "reflect" may yield incorrect results on '
........................................................................................................................................................................................................................................................................................................F..F.........................................................Use
minimum degree ordering on A'+A.
.....................................Use minimum degree ordering on A'+A.
.....................................Use minimum degree ordering on A'+A.
................................Use minimum degree ordering on A'+A.
....................................................................................................................................................................................................................................................................................................................................................0.2
0.2
0.2
......0.2
..0.2
0.2
0.2
0.2
0.2
.........................................................................................................................................................................................................Ties
preclude use of exact statistic.
..Ties preclude use of exact statistic.
......
======================================================================
FAIL: test_explicit (scipy.tests.test_odr.test_odr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py",
line 50, in test_explicit
    -8.7849712165253724e-02]),
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([  1.26462971e+03,  -5.42545890e+01,  -8.64250389e-02])
 y: array([  1.26465481e+03,  -5.40184100e+01,  -8.78497122e-02])

======================================================================
FAIL: test_multi (scipy.tests.test_odr.test_odr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py",
line 191, in test_multi
    0.5101147161764654,  0.5173902330489161]),
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
232, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line
217, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 4.31272063,  2.44289312,  7.76215871,  0.55995622,  0.46423343])
 y: array([ 4.37998803,  2.43330576,  8.00288459,  0.51011472,  0.51739023])

----------------------------------------------------------------------
Ran 1728 tests in 3.660s

FAILED (failures=2)
<unittest._TextTestResult run=1728 errors=0 failures=2>



--------------------------------------------------------------------------------------------------------------
2. System check
--------------------------------------------------------------------------------------------------------------
yutec@yutec-laptop:~$ python -c 'import os,sys;print os.name,sys.platform'
posix linux2

yutec@yutec-laptop:~$ uname -a
Linux yutec-laptop 2.6.22-14-generic #1 SMP Sun Oct 14 21:45:15 GMT
2007 x86_64 GNU/Linux

yutec@yutec-laptop:~$ gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v
--enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr
--enable-shared --with-system-zlib --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --enable-nls
--with-gxx-include-dir=/usr/include/c++/4.1.3 --program-suffix=-4.1
--enable-__cxa_atexit --enable-clocale=gnu --enable-libstdcxx-debug
--enable-mpfr --enable-checking=release x86_64-linux-gnu
Thread model: posix
gcc version 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)

yutec@yutec-laptop:~$ g77 --version
GNU Fortran (GCC) 3.4.6 (Ubuntu 3.4.6-6ubuntu2)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
or type the command `info -f g77 Copying'.

yutec@yutec-laptop:~$ python -c 'import sys;print sys.version'
2.5.1 (r251:54863, Oct  5 2007, 13:50:07)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)]

yutec@yutec-laptop:~$ python -c 'import numpy;print numpy.__version__'
1.0.4

yutec@yutec-laptop:~$ cd /usr/lib/python2.5/site-packages/scipy/

yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd linalg
yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$
yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$
python setup_atlas_version.py build_ext --inplace --force
Traceback (most recent call last):
  File "setup_atlas_version.py", line 7, in <module>
    from numpy.distutils.misc_util import get_path, default_config_dict
ImportError: cannot import name get_path

yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$
python -c 'import atlas_version'
ATLAS version 3.6.0 built by root on Thu Jun  3 21:13:07 UTC 2004:
   UNAME    : Linux ravel 2.6.5 #3 SMP Tue Apr 13 13:41:54 UTC 2004
x86_64 GNU/Linux
   INSTFLG  :
   MMDEF    : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm
   ARCHDEF  : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc
   F2CDEFS  : -DAdd__ -DStringSunStyle
   CACHEEDGE: 720896
   F77      : /home/camm/usr/bin/g77, version GNU Fortran (GCC) 3.3.3
(Debian 20040422)
   F77FLAGS : -fomit-frame-pointer -O -m64
   CC       : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422)
   CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64
   MCC      : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422)
   MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64

yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ cd ..
yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd ..
yutec@yutec-laptop:/usr/lib/python2.5/site-packages$ cd numpy
yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy$ cd distutils/

yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy/distutils$
python system_info.py
lapack_info:
  libraries lapack not found in /usr/local/lib
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/lib']
    language = f77

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas
  libraries lapack_atlas not found in /usr/lib/atlas
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
__main__.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/atlas
  libraries lapack_atlas not found in /usr/lib/atlas
__main__.atlas_info
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib']
    language = f77
    include_dirs = ['/usr/include']

customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
    include_dirs = ['/usr/include']

lapack_atlas_info:
  libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/lib/atlas
  libraries lapack_atlas not found in /usr/lib/atlas
__main__.lapack_atlas_info
  FOUND:
    libraries = ['lapack', 'lapack_atlas', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib']
    language = f77
    include_dirs = ['/usr/include']

umfpack_info:
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
  NOT AVAILABLE

_pkg_config_info:
Found executable /usr/bin/pkg-config
  NOT AVAILABLE

lapack_atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib/atlas
  libraries lapack_atlas not found in /usr/lib/atlas
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib
__main__.lapack_atlas_threads_info
  NOT AVAILABLE

x11_info:
  libraries X11 not found in /usr/lib64
  NOT AVAILABLE

blas_info:
  libraries blas not found in /usr/local/lib
  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib']
    language = f77

fftw_info:
  libraries fftw3 not found in /usr/local/lib
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

f2py_info:
  FOUND:
    sources = ['/usr/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.c']
    include_dirs = ['/usr/lib/python2.5/site-packages/numpy/f2py/src']

gdk_pixbuf_xlib_2_info:
  NOT AVAILABLE

dfftw_threads_info:
  libraries drfftw_threads,dfftw_threads not found in /usr/local/lib
  libraries drfftw_threads,dfftw_threads not found in /usr/lib
  dfftw threads not found
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib/atlas
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib']
    language = c
    include_dirs = ['/usr/include']

fftw3_info:
  libraries fftw3 not found in /usr/local/lib
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
    include_dirs = ['/usr/include']

sfftw_info:
  libraries srfftw,sfftw not found in /usr/local/lib
  libraries srfftw,sfftw not found in /usr/lib
  sfftw not found
  NOT AVAILABLE

xft_info:
  NOT AVAILABLE

fft_opt_info:
djbfft_info:
  NOT AVAILABLE

  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

gdk_x11_2_info:
  NOT AVAILABLE

agg2_info:
  NOT AVAILABLE

numarray_info:
  NOT AVAILABLE

blas_src_info:
  NOT AVAILABLE

fftw2_info:
  libraries rfftw,fftw not found in /usr/local/lib
  FOUND:
    libraries = ['rfftw', 'fftw']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW_H', None)]
    include_dirs = ['/usr/include']

fftw_threads_info:
  libraries rfftw_threads,fftw_threads not found in /usr/local/lib
  FOUND:
    libraries = ['rfftw_threads', 'fftw_threads']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW_THREADS_H', None)]
    include_dirs = ['/usr/include']

_numpy_info:
  FOUND:
    define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'), ('NUMERIC', None)]
    include_dirs = ['/usr/include/python2.5']

wx_info:
Could not locate executable wx-config
File not found: None. Cannot determine wx info.
  NOT AVAILABLE

gdk_info:
  NOT AVAILABLE

gtkp_x11_2_info:
  NOT AVAILABLE

sfftw_threads_info:
  libraries srfftw_threads,sfftw_threads not found in /usr/local/lib
  libraries srfftw_threads,sfftw_threads not found in /usr/lib
  sfftw threads not found
  NOT AVAILABLE

boost_python_info:
  NOT AVAILABLE

freetype2_info:
  NOT AVAILABLE

gdk_2_info:
  NOT AVAILABLE

dfftw_info:
  libraries drfftw,dfftw not found in /usr/local/lib
  libraries drfftw,dfftw not found in /usr/lib
  dfftw not found
  NOT AVAILABLE

lapack_src_info:
  NOT AVAILABLE

gtkp_2_info:
  NOT AVAILABLE

gdk_pixbuf_2_info:
  NOT AVAILABLE

amd_info:
  libraries amd not found in /usr/local/lib
  libraries amd not found in /usr/lib
  NOT AVAILABLE

Numeric_info:
  FOUND:
    define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'), ('NUMERIC', None)]
    include_dirs = ['/usr/include/python2.5']

numerix_info:
numpy_info:
  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.0.4\\""'), ('NUMPY', None)]

  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.0.4\\""'), ('NUMPY', None)]


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