[SciPy-user] scipy 0.6 installation problem
Yutec Sun
dbm.sun at gmail.com
Fri Nov 23 12:18:03 EST 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 at 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 at yutec-laptop:~$ python -c 'import os,sys;print os.name,sys.platform'
posix linux2
yutec at 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 at 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 at 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 at 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 at yutec-laptop:~$ python -c 'import numpy;print numpy.__version__'
1.0.4
yutec at yutec-laptop:~$ cd /usr/lib/python2.5/site-packages/scipy/
yutec at yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd linalg
yutec at yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$
yutec at 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 at 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 at yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ cd ..
yutec at yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd ..
yutec at yutec-laptop:/usr/lib/python2.5/site-packages$ cd numpy
yutec at yutec-laptop:/usr/lib/python2.5/site-packages/numpy$ cd distutils/
yutec at 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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