Re: error importing scipy
Chiara Caronna <chiaracaronna <at> hotmail.com>
2007-02-01 17:31:44 GMT
>From: Robert Kern <robert.kern <at> gmail.com>
>Reply-To: SciPy Users List <scipy-user <at> scipy.org>
>To: SciPy Users List <scipy-user <at> scipy.org>
>Subject: Re: [SciPy-user] error importing scipy
>Date: Thu, 01 Feb 2007 10:56:14 -0600
>
>Chiara Caronna wrote:
> > Hello,
> > since a couple of days I got an error when I try to run "from scipy
>import
> > *"
> > here is the error message....
> >
> >
> > " Traceback (most recent call last):
> > File "<stdin>", line 1, in ?
> > File
>"/usr/local/lib/python2.4/site-packages/scipy/linalg/__init__.py",
> > line 8, in ?
> > from basic import *
> > File "/usr/local/lib/python2.4/site-packages/scipy/linalg/basic.py",
>line
> > 227, in ?
> > import decomp
> > File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py",
>line
> > 21, in ?
> > from blas import get_blas_funcs
> > File "/usr/local/lib/python2.4/site-packages/scipy/linalg/blas.py",
>line
> > 14, in ?
> > from scipy.linalg import fblas
> > ImportError:
>/usr/local/lib/python2.4/site-packages/scipy/linalg/fblas.so:
> > undefined symbol: srotmg_"
> >
> > does anyone have a clue?!
>
>Your scipy was not linked to a BLAS library correctly. What BLAS library
>were
>you trying to link against?
'_' ... I have never tried to do that... at least I am not aware of...
Where are its files located on your system?
I don't know it, how can I find that out?
>Did you use a site.cfg file to configure scipy?
I am not sure I understood the question... I download the file
scipy-0.5.2.tar.gz, extracted it and followed the instructions... so I guess
the answer is "no, I didn't"
Can you show us the output of
>
> $ cd ~/src/scipy # or whatever
> $ python setup.py configure
I did this:
cd /usr/local/lib/python2.4/site-packages/scipy
python setup.py configure
here is the output:
non-existing path in 'cluster': 'src/vq_wrap.cpp'
Appending scipy.cluster configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.cluster')
mkl_info:
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
fftw3_info:
libraries fftw3 not found in /usr/local/lib
libraries fftw3 not found in /usr/lib
fftw3 not found
NOT AVAILABLE
fftw2_info:
libraries rfftw,fftw not found in /usr/local/lib
libraries rfftw,fftw not found in /usr/lib
fftw2 not found
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
djbfft_info:
NOT AVAILABLE
could not resolve pattern in 'fftpack': 'dfftpack/*.f'
non-existing path in 'fftpack': 'fftpack.pyf'
non-existing path in 'fftpack': 'src/zfft.c'
non-existing path in 'fftpack': 'src/drfft.c'
non-existing path in 'fftpack': 'src/zrfft.c'
non-existing path in 'fftpack': 'src/zfftnd.c'
non-existing path in 'fftpack': 'convolve.pyf'
non-existing path in 'fftpack': 'src/convolve.c'
Appending scipy.fftpack configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.fftpack')
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 lapack,blas not found in /usr/local/lib
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
Could not locate executable gfortran
Could not locate executable f95
customize GnuFCompiler
invalid command 'configure'
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
customize IntelFCompiler
invalid command 'configure'
customize LaheyFCompiler
invalid command 'configure'
customize PGroupFCompiler
invalid command 'configure'
customize AbsoftFCompiler
invalid command 'configure'
customize NAGFCompiler
invalid command 'configure'
customize VastFCompiler
invalid command 'configure'
customize CompaqFCompiler
invalid command 'configure'
customize IntelItaniumFCompiler
invalid command 'configure'
customize IntelEM64TFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize G95FCompiler
invalid command 'configure'
customize GnuFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize GnuFCompiler
customize GnuFCompiler using config
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
could not resolve pattern in 'integrate': 'linpack_lite/*.f'
could not resolve pattern in 'integrate': 'mach/*.f'
could not resolve pattern in 'integrate': 'quadpack/*.f'
could not resolve pattern in 'integrate': 'odepack/*.f'
non-existing path in 'integrate': '_quadpackmodule.c'
non-existing path in 'integrate': '_odepackmodule.c'
non-existing path in 'integrate': 'vode.pyf'
Appending scipy.integrate configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.integrate')
could not resolve pattern in 'interpolate': 'fitpack/*.f'
non-existing path in 'interpolate': '_fitpackmodule.c'
non-existing path in 'interpolate': 'fitpack.pyf'
Appending scipy.interpolate configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.interpolate')
non-existing path in 'io': 'numpyiomodule.c'
Appending scipy.io configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.io')
ATLAS version ?.?.?
non-existing path in 'lib/blas': 'fblas.pyf.src'
non-existing path in 'lib/blas': 'fblaswrap.f.src'
could not resolve pattern in 'lib/blas': 'fblas_l?.pyf.src'
non-existing path in 'lib/blas': 'cblas.pyf.src'
could not resolve pattern in 'lib/blas': 'cblas_l?.pyf.src'
Appending scipy.lib.blas configuration to scipy.lib
Ignoring attempt to set 'name' (from 'scipy.lib' to 'scipy.lib.blas')
lapack_opt_info:
lapack_mkl_info:
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack,blas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'lapack', 'blas']
library_dirs = ['/usr/lib']
language = f77
customize GnuFCompiler
invalid command 'configure'
customize IntelFCompiler
invalid command 'configure'
customize LaheyFCompiler
invalid command 'configure'
customize PGroupFCompiler
invalid command 'configure'
customize AbsoftFCompiler
invalid command 'configure'
customize NAGFCompiler
invalid command 'configure'
customize VastFCompiler
invalid command 'configure'
customize CompaqFCompiler
invalid command 'configure'
customize IntelItaniumFCompiler
invalid command 'configure'
customize IntelEM64TFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize G95FCompiler
invalid command 'configure'
customize GnuFCompiler
invalid command 'configure'
customize Gnu95FCompiler
invalid command 'configure'
customize GnuFCompiler
customize GnuFCompiler using config
FOUND:
libraries = ['lapack', 'lapack', 'blas']
library_dirs = ['/usr/lib']
language = f77
define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
ATLAS version ?.?.?
non-existing path in 'lib/lapack': 'flapack.pyf.src'
could not resolve pattern in 'lib/lapack': 'flapack_*.pyf.src'
non-existing path in 'lib/lapack': 'clapack.pyf.src'
non-existing path in 'lib/lapack': 'calc_lwork.f'
non-existing path in 'lib/lapack': 'atlas_version.c'
Appending scipy.lib.lapack configuration to scipy.lib
Ignoring attempt to set 'name' (from 'scipy.lib' to 'scipy.lib.lapack')
Appending scipy.lib configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.lib')
ATLAS version ?.?.?
non-existing path in 'linalg': 'src/fblaswrap.f'
non-existing path in 'linalg': 'generic_fblas.pyf'
non-existing path in 'linalg': 'generic_fblas1.pyf'
non-existing path in 'linalg': 'generic_fblas2.pyf'
non-existing path in 'linalg': 'generic_fblas3.pyf'
non-existing path in 'linalg': 'generic_cblas.pyf'
non-existing path in 'linalg': 'generic_cblas1.pyf'
non-existing path in 'linalg': 'generic_flapack.pyf'
non-existing path in 'linalg': 'flapack_user_routines.pyf'
non-existing path in 'linalg': 'generic_clapack.pyf'
non-existing path in 'linalg': 'src/det.f'
non-existing path in 'linalg': 'src/lu.f'
non-existing path in 'linalg': 'src/calc_lwork.f'
non-existing path in 'linalg': 'atlas_version.c'
non-existing path in 'linalg': 'iterative/STOPTEST2.f.src'
non-existing path in 'linalg': 'iterative/getbreak.f.src'
non-existing path in 'linalg': 'iterative/BiCGREVCOM.f.src'
non-existing path in 'linalg': 'iterative/BiCGSTABREVCOM.f.src'
non-existing path in 'linalg': 'iterative/CGREVCOM.f.src'
non-existing path in 'linalg': 'iterative/CGSREVCOM.f.src'
non-existing path in 'linalg': 'iterative/GMRESREVCOM.f.src'
non-existing path in 'linalg': 'iterative/QMRREVCOM.f.src'
non-existing path in 'linalg': 'iterative/_iterative.pyf.src'
Appending scipy.linalg configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.linalg')
could not resolve pattern in 'linsolve': 'SuperLU/SRC/*.c'
non-existing path in 'linsolve': '_zsuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_dsuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_csuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
non-existing path in 'linsolve': '_ssuperlumodule.c'
non-existing path in 'linsolve': '_superlu_utils.c'
non-existing path in 'linsolve': '_superluobject.c'
umfpack_info:
libraries umfpack not found in /usr/local/lib
libraries umfpack not found in /usr/lib
/usr/local/lib/python2.4/site-packages/numpy/distutils/system_info.py:401:
UserWarning:
UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/)
not found. Directories to search for the libraries can be specified in
the
numpy/distutils/site.cfg file (section [umfpack]) or by setting
the UMFPACK environment variable.
warnings.warn(self.notfounderror.__doc__)
NOT AVAILABLE
non-existing path in 'linsolve/umfpack': 'umfpack.i'
non-existing path in 'linsolve/umfpack': 'umfpack.i'
Appending scipy.linsolve.umfpack configuration to scipy.linsolve
Ignoring attempt to set 'name' (from 'scipy.linsolve' to
'scipy.linsolve.umfpack')
Appending scipy.linsolve configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.linsolve')
non-existing path in 'maxentropy': 'doc'
Appending scipy.maxentropy configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.maxentropy')
Appending scipy.misc configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.misc')
non-existing path in 'odr': 'odrpack/d_odr.f'
non-existing path in 'odr': 'odrpack/d_mprec.f'
non-existing path in 'odr': 'odrpack/dlunoc.f'
non-existing path in 'odr': 'odrpack/d_lpk.f'
non-existing path in 'odr': '__odrpack.c'
Appending scipy.odr configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.odr')
could not resolve pattern in 'optimize': 'minpack/*f'
non-existing path in 'optimize': '_minpackmodule.c'
could not resolve pattern in 'optimize': 'Zeros/*.c'
non-existing path in 'optimize': 'zeros.c'
non-existing path in 'optimize': 'lbfgsb/lbfgsb.pyf'
non-existing path in 'optimize': 'lbfgsb/routines.f'
non-existing path in 'optimize': 'tnc/moduleTNC.c'
non-existing path in 'optimize': 'tnc/tnc.c'
non-existing path in 'optimize': 'cobyla/cobyla.pyf'
non-existing path in 'optimize': 'cobyla/cobyla2.f'
non-existing path in 'optimize': 'cobyla/trstlp.f'
non-existing path in 'optimize': 'minpack2/minpack2.pyf'
non-existing path in 'optimize': 'minpack2/dcsrch.f'
non-existing path in 'optimize': 'minpack2/dcstep.f'
Appending scipy.optimize configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.optimize')
Appending scipy.sandbox configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.sandbox')
non-existing path in 'signal': 'sigtoolsmodule.c'
non-existing path in 'signal': 'firfilter.c'
non-existing path in 'signal': 'medianfilter.c'
non-existing path in 'signal': 'sigtools.h'
non-existing path in 'signal': 'splinemodule.c'
non-existing path in 'signal': 'S_bspline_util.c'
non-existing path in 'signal': 'D_bspline_util.c'
non-existing path in 'signal': 'C_bspline_util.c'
non-existing path in 'signal': 'Z_bspline_util.c'
non-existing path in 'signal': 'bspline_util.c'
Appending scipy.signal configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.signal')
non-existing path in 'sparse': 'sparsetools/spblas.f.src'
non-existing path in 'sparse': 'sparsetools/spconv.f.src'
non-existing path in 'sparse': 'sparsetools/sparsetools.pyf.src'
Appending scipy.sparse configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.sparse')
could not resolve pattern in 'special': 'c_misc/*.c'
could not resolve pattern in 'special': 'cephes/*.c'
could not resolve pattern in 'special': 'mach/*.f'
could not resolve pattern in 'special': 'amos/*.f'
could not resolve pattern in 'special': 'toms/*.f'
could not resolve pattern in 'special': 'cdflib/*.f'
could not resolve pattern in 'special': 'specfun/*.f'
non-existing path in 'special': '_cephesmodule.c'
non-existing path in 'special': 'amos_wrappers.c'
non-existing path in 'special': 'specfun_wrappers.c'
non-existing path in 'special': 'toms_wrappers.c'
non-existing path in 'special': 'cdf_wrappers.c'
non-existing path in 'special': 'ufunc_extras.c'
non-existing path in 'special': 'specfun.pyf'
Appending scipy.special configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.special')
could not resolve pattern in 'stats': 'statlib/*.f'
non-existing path in 'stats': 'statlib.pyf'
non-existing path in 'stats': 'futil.f'
non-existing path in 'stats': 'mvn.pyf'
non-existing path in 'stats': 'mvndst.f'
Appending scipy.stats configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.stats')
non-existing path in 'ndimage': 'src/nd_image.c'
non-existing path in 'ndimage': 'src/ni_filters.c'
non-existing path in 'ndimage': 'src/ni_fourier.c'
non-existing path in 'ndimage': 'src/ni_interpolation.c'
non-existing path in 'ndimage': 'src/ni_measure.c'
non-existing path in 'ndimage': 'src/ni_morphology.c'
non-existing path in 'ndimage': 'src/ni_support.c'
non-existing path in 'ndimage': 'src'
Appending scipy.ndimage configuration to scipy
Ignoring attempt to set 'name' (from 'scipy' to 'scipy.ndimage')
Warning: Assuming default configuration
(stsci/convolve/{setup_convolve,setup}.py was not
found)
Traceback (most recent call last):
File "setup.py", line 31, in ?
setup(**configuration(top_path='').todict())
File "setup.py", line 23, in configuration
config.add_subpackage('stsci')
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
765, in add_subpackage
caller_level = 2)
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
748, in get_subpackage
caller_level = caller_level + 1)
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
695, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "/usr/local/lib/python2.4/site-packages/scipy/stsci/setup.py", line
5, in configuration
config.add_subpackage('convolve')
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
765, in add_subpackage
caller_level = 2)
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
741, in get_subpackage
caller_level = caller_level+1)
File
"/usr/local/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line
541, in __init__
raise ValueError("%r is not a directory" % (package_path,))
ValueError: 'stsci/convolve' is not a directory
>
>--
>Robert Kern
>
>"I have come to believe that the whole world is an enigma, a harmless
>enigma
> that is made terrible by our own mad attempt to interpret it as though it
>had
> an underlying truth."
> -- Umberto Eco
>_______________________________________________
>SciPy-user mailing list
>SciPy-user <at> scipy.org
>http://projects.scipy.org/mailman/listinfo/scipy-user
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