[SciPy-user] scipy 0.6 installation problem

Andrew Straw strawman@astraw....
Sun Nov 25 23:35:55 CST 2007


Hi Yutec,

You can install my version:

http://debs.astraw.com/gutsy/python-scipy_0.6.0-1ubuntu0~0ads2_amd64.deb

-Andrew

Yutec Sun wrote:
> 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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