[SciPy-user] scipy install fails: numpy.ndarray

James K. Gruetzner jkgruet at sandia.gov
Tue Feb 14 15:03:52 CST 2006


Any ideas how to correct this?  I've just installed scipy 0.4.4, and am 
having some problems with it.  The key appears to be in the references 
to numpy.ndarray.

When running scipy.test(level=0), numerous errors of:
     AttributeError: 'numpy.ndarray' object has no attribute 'dtypechar'

Installation of scipy 0.4.4 does have many warnings, but appears to 
complete OK. 
   - Many warnings that variables "might be used uninitialized" in 
various functions.
   - Many warnings that "ignoring return value of 'fscanf'"
   - Several warnings that "POSIX_C_SOURCE" redefined.
   - Many "unused variable" warnings

Information follows below.

Thanks in advance.
     James
----------------------------
system/platform:  posix linux2
Fedora Core 4
python 2.4.1
numpy 0.9.4
LAPACK
ATLAS 3.7.11  NOTE 1
gcc 4.0.2
fftw 3.0.1

1. Installed in the local tree.  In ../scipy/Lib/linalg, the command
      python setup_atlas_version.py build_ext --inplace --force
fails with the error message:    
/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py:896: 
UserWarning: Use Configuration('linalg','',top_path=None) instead of 
deprecated default_config_dict('linalg','',None)
  warnings.warn('Use Configuration(%s,%s,top_path=%s) instead of '\
Traceback (most recent call last):
  File "setup_atlas_version.py", line 29, in ?
    setup(**configuration())
  File "setup_atlas_version.py", line 13, in configuration
    del config['fortran_libraries']
KeyError: 'fortran_libraries'

-----------------
Output of python INSTALLDIR/numpy/distutils/system_info.py command:



_pkg_config_info:
  NOT AVAILABLE

agg2_info:
( src_dirs = .:/usr/local/src )
  NOT AVAILABLE

atlas_blas_info:
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libf77blas.a )
( paths: /usr/local/lib/atlas/libcblas.a )
( paths: /usr/local/lib/atlas/libatlas.a )
( include_dirs = /usr/local/include:/usr/include )
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/lib/atlas']
    language = c

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libatlas.a )
  NOT AVAILABLE

atlas_info:
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libf77blas.a )
( paths: /usr/local/lib/atlas/libcblas.a )
( paths: /usr/local/lib/atlas/libatlas.a )
( paths: /usr/local/lib/atlas/liblapack.a )
system_info.atlas_info
( include_dirs = /usr/local/include:/usr/include )
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/lib/atlas']
    language = f77

atlas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libatlas.a )
system_info.atlas_threads_info
  NOT AVAILABLE

blas_info:
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/libblas.a )
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/local/lib']
    language = f77

blas_mkl_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  NOT AVAILABLE

blas_opt_info:
running build_src
building extension "atlas_version" sources
  adding 'build/src/atlas_version_-0x32261224.c' to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/lib/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]

blas_src_info:
( src_dirs = .:/usr/local/src )
  NOT AVAILABLE

boost_python_info:
( src_dirs = .:/usr/local/src )
  NOT AVAILABLE

dfftw_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  dfftw not found
  NOT AVAILABLE

dfftw_threads_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  dfftw threads not found
  NOT AVAILABLE

djbfft_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  NOT AVAILABLE

fft_opt_info:
fftw3_info:
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/local/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/local/include']

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

fftw2_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  fftw2 not found
  NOT AVAILABLE

fftw_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
( paths: /usr/local/lib/libfftw3.a )
( paths: /usr/local/include/fftw3.h )
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/local/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/local/include']

fftw_threads_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  fftw threads not found
  NOT AVAILABLE

freetype2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['freetype', 'z']
    define_macros = [('FREETYPE2_INFO', '"\\"9.7.3\\""'), 
('FREETYPE2_VERSION_9_7_3', None)]
    include_dirs = ['/usr/include/freetype2']

gdk_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 
'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    define_macros = [('GDK_2_INFO', '"\\"2.6.10\\""'), 
('GDK_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), 
('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', 
'/usr/X11R6/include', '/usr/include/pango-1.0', 
'/usr/include/freetype2', '/usr/include/freetype2/config', 
'/usr/include/glib-2.0', '/usr/lib/glib-2.0/include']

gdk_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gdk', 'Xi', 'Xext', 'X11', 'm', 'glib']
    library_dirs = ['/usr/X11R6/lib']
    define_macros = [('GDK_INFO', '"\\"1.2.10\\""'), 
('GDK_VERSION_1_2_10', None)]
    include_dirs = ['/usr/include/gtk-1.2', '/usr/X11R6/include', 
'/usr/include/glib-1.2', '/usr/lib/glib/include']

gdk_pixbuf_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 
'dl', 'glib-2.0']
    define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.6.10\\""'), 
('GDK_PIXBUF_VERSION_2_6_10', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', 
'/usr/lib/glib-2.0/include']

gdk_pixbuf_xlib_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 
'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.6.10\\""'), 
('GDK_PIXBUF_XLIB_VERSION_2_6_10', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', 
'/usr/lib/glib-2.0/include']

gdk_x11_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 
'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    define_macros = [('GDK_X11_2_INFO', '"\\"2.6.10\\""'), 
('GDK_X11_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', 
None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', 
'/usr/X11R6/include', '/usr/include/pango-1.0', 
'/usr/include/freetype2', '/usr/include/freetype2/config', 
'/usr/include/glib-2.0', '/usr/lib/glib-2.0/include']

gtkp_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 
'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 
'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    define_macros = [('GTKP_2_INFO', '"\\"2.6.10\\""'), 
('GTK_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), 
('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', 
'/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', 
'/usr/include/freetype2', '/usr/include/freetype2/config', 
'/usr/include/glib-2.0', '/usr/lib/glib-2.0/include']

gtkp_x11_2_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 
'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 
'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    define_macros = [('GTKP_X11_2_INFO', '"\\"2.6.10\\""'), 
('GTK_X11_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', 
None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', 
'/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', 
'/usr/include/freetype2', '/usr/include/freetype2/config', 
'/usr/include/glib-2.0', '/usr/lib/glib-2.0/include']

lapack_atlas_info:
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libf77blas.a )
( paths: /usr/local/lib/atlas/libcblas.a )
( paths: /usr/local/lib/atlas/libatlas.a )
system_info.lapack_atlas_info
  NOT AVAILABLE

lapack_atlas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/atlas )
( paths: /usr/lib/sse2 )
( paths: /usr/local/lib/atlas/libatlas.a )
system_info.lapack_atlas_threads_info
  NOT AVAILABLE

lapack_info:
( library_dirs = /usr/local/lib:/usr/lib )
( paths: /usr/local/lib/liblapack.a )
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/local/lib']
    language = f77

lapack_mkl_info:
mkl_info:
  NOT AVAILABLE

  NOT AVAILABLE

lapack_opt_info:
running build_src
building extension "atlas_version" sources
  adding 'build/src/atlas_version_0x39ddef23.c' to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_ext
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/lib/atlas']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]

lapack_src_info:
( src_dirs = .:/usr/local/src )
( paths: /usr/local/src/LAPACK/SRC )
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    sources = ['/usr/local/src/LAPACK/SRC/sbdsdc.f', 
'/usr/local/src/LAPAC ...
... /LAPACK/SRC/izmax1.f', '/usr/local/src/LAPACK/SRC/dzsum1.f']
    language = f77

numarray_info:
( include_dirs = /usr/include/python2.4 )
( paths: /usr/include/python2.4/numarray/arrayobject.h )
( library_dirs =  )
  FOUND:
    define_macros = [('NUMARRAY_VERSION', '"\\"1.5.1\\""'), ('NUMARRAY', 
None)]
    include_dirs = ['/usr/include/python2.4']

numpy_info:
( include_dirs = /usr/include/python2.4 )
( library_dirs =  )
  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"0.9.4\\""'), ('NUMPY', None)]

sfftw_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  sfftw not found
  NOT AVAILABLE

sfftw_threads_info:
( library_dirs = /usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include )
  sfftw threads not found
  NOT AVAILABLE

wx_info:
Could not locate executable wx-config
File not found: wx-config. Cannot determine wx info.
  NOT AVAILABLE

x11_info:
( library_dirs = /usr/X11R6/lib:/usr/lib )
( include_dirs = /usr/X11R6/include:/usr/include )
( paths: /usr/X11R6/lib/libX11.so )
( paths: /usr/X11R6/include/X11/X.h )
( library_dirs = /usr/X11R6/lib:/usr/lib )
  FOUND:
    libraries = ['X11']
    library_dirs = ['/usr/X11R6/lib']
    include_dirs = ['/usr/X11R6/include']

xft_info:
( library_dirs = /usr/local/lib:/usr/lib )
  FOUND:
    libraries = ['Xft', 'X11', 'freetype', 'Xrender', 'fontconfig']
    library_dirs = ['/usr/X11R6/lib']
    define_macros = [('XFT_INFO', '"\\"2.1.2.2\\""'), 
('XFT_VERSION_2_1_2_2', None)]
    include_dirs = ['/usr/X11R6/include', '/usr/include/freetype2', 
'/usr/include/freetype2/config']





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