[SciPy-user] scipy 0.6 installation problem

Johann Cohen-Tanugi cohen@slac.stanford....
Fri Nov 23 13:30:41 CST 2007


well, I am certainly no expert on scipy, but the results of the test 
don't look that bad! When something really bad has occurred at build 
time, you usually don't pass almost all the tests!

Ran 1728 tests in 3.660s
FAILED (failures=2) <unittest._TextTestResult run=1728 errors=0 failures=2>

As for the one that you don't pass, it seems that you end up with odr evaluations different than the ones the test expects... I think I have the same issue, but it does not point, IMHO, to a failure to build correctly.

Experts will tell you about it better than I can, but from your post it 
seems that you are mostly ok to start enjoying scipy
best,
Johann


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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>   



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