[SciPy-user] Installing scipy-5.2 on fedora 64 bit: cannot import name flapack

Niels L Ellegaard niels.ellegaard at gmail.com
Sat Dec 16 00:21:11 CST 2006


Dear masters

I am trying to install scipy 5.2 on a fedora 64 bit machine with 
numpy 1.0.1. When I try to run scipy.test() i get the following error

    from scipy.linalg import flapack
ImportError: cannot import name flapack

I must be doing something wrong, but I cannot see what, so I would
 be grateful for some hints (Details below.. sorry about the flood)

                         Thanks in advance

                                    Niels

***************** Output from scipy.test() ************

 python -c 'import scipy; scipy.test()'
  Found 4 tests for scipy.io.array_import
  Found 397 tests for scipy.ndimage
  Found 96 tests for scipy.sparse.sparse
  Found 20 tests for scipy.fftpack.pseudo_diffs
  Found 6 tests for scipy.optimize.optimize
  Found 6 tests for scipy.interpolate.fitpack
  Found 6 tests for scipy.interpolate
  Found 12 tests for scipy.io.mmio
  Found 18 tests for scipy.fftpack.basic
  Found 4 tests for scipy.io.recaster
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' 
from
'.../linsolve/umfpack/__init__.pyc'>
/usr/lib64/python2.4/site-packages/scipy/linsolve/umfpack/tests/
test_umfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 4 tests for scipy.optimize.zeros
  Found 28 tests for scipy.io.mio
Warning: FAILURE importing tests for <module 'scipy.special.basic' from
'...ckages/scipy/special/basic.pyc'>
/usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py:17: ImportError:
cannot import name flapack (in ?)
Warning: FAILURE importing tests for <module 'scipy.lib.blas.fblas' from
'...ckages/scipy/lib/blas/fblas.so'>
/usr/lib64/python2.4/site-packages/scipy/lib/blas/__init__.py:10: 
ImportError:
/usr/lib64/python2.4/site-packages/scipy/lib/blas/cblas.so: undefined symbol:
cblas_saxpy (in ?)
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack'
from '...y/linsolve/umfpack/umfpack.pyc'>
/usr/lib64/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_
mfpack.py:17:
AttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 1 tests for scipy.optimize.cobyla
  Found 4 tests for scipy.fftpack.helper
  Found 0 tests for __main__

Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
...E.........................................................................
............................................................................
.............................................................................
.............................................................................
.............................................................................
..........................Resizing...
16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
........................Use minimum degree ordering on A'+A.
...................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
.................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
......................................
/usr/lib64/python2.4/site-packages/scipy/interpolate/fitpack2.py:457:
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)
.......................................................................
............
======================================================================
ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python2.4/site-packages/scipy/io/tests/test_array_import.py",
line 55, in check_integer
    from scipy import stats
  File "/usr/lib64/python2.4/site-packages/scipy/stats/__init__.py", line 7, in ?
    from stats import *
  File "/usr/lib64/python2.4/site-packages/scipy/stats/stats.py", line 190, in ?
   import scipy.special as special
  File "/usr/lib64/python2.4/site-packages/scipy/special/__init__.py", line 10, in ?
    import orthogonal
  File "/usr/lib64/python2.4/site-packages/scipy/special/orthogonal.py", line
65, in ?
    from scipy.linalg import eig
  File "/usr/lib64/python2.4/site-packages/scipy/linalg/__init__.py", line 8, in ?
    from basic import *
  File "/usr/lib64/python2.4/site-packages/scipy/linalg/basic.py", line 17, in ?
   from lapack import get_lapack_funcs
  File "/usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py", line 17, in ?
    from scipy.linalg import flapack
ImportError: cannot import name flapack

----------------------------------------------------------------------
Ran 606 tests in 2.998s

FAILED (errors=1)

*************** Site.cfg *************

[lapack]
library_dirs = /usr/lib64

[atlas]
library_dirs = /usr/lib64:/usr/lib64/atlas

[blas]
library_dirs = /usr/lib64:/usr/lib64/atlas

[umfpack]
library_dirs = /usr/lib64
include_dirs = /usr/include/ufsparse/

[amd]
library_dirs = /usr/lib64

[fftw]
library_dirs = /usr/lib64/

[fftw2]
library_dirs = /usr/lib64/

[fftw3]
library_dirs = /usr/lib64/


**************** Output from installation *******
python setup.py install > log.0
Warning: Subpackage 'Lib' configuration returned as 'scipy'

cat log.0
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:
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib64/']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

djbfft_info:
  NOT AVAILABLE

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
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'blas']
    library_dirs = ['/usr/lib64/atlas']
    language = c
    include_dirs = ['/usr/include/atlas']

customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy_distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4
-m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/lib64/atlas -llapack -lblas -o _configtest
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
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'blas']
    library_dirs = ['/usr/lib64/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')]
    include_dirs = ['/usr/include/atlas']

ATLAS version 3.6.0
lapack_opt_info:
lapack_mkl_info:
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'lapack', 'blas']
    library_dirs = ['/usr/lib64/atlas']
    language = f77
    include_dirs = ['/usr/include/atlas']

customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy_distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4
-m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/lib64/atlas -llapack -llapack -lblas -o
_configtest
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
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'lapack', 'blas']
    library_dirs = ['/usr/lib64/atlas']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')]
    include_dirs = ['/usr/include/atlas']

ATLAS version 3.6.0
ATLAS version 3.6.0
non-existing path in 'Lib/linsolve': 'tests'
umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/lib64']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/usr/lib64']
    swig_opts = ['-I/usr/include/ufsparse']
    define_macros = [('SCIPY_UMFPACK_H', None)]
    include_dirs = ['/usr/include/ufsparse']

non-existing path in 'Lib/maxentropy': 'doc'
running install
running build
running config_fc
running build_src
building py_modules sources
building library "dfftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "fitpack" sources
building library "superlu_src" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "c_misc" sources
building library "cephes" sources
building library "mach" sources
building library "toms" sources
building library "amos" sources
building library "cdf" sources
building library "specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
  adding 'build/src.linux-x86_64-2.4/Lib/interpolate/dfitpack-
f2pywrappers.f' to
sources.
building extension "scipy.io.numpyio" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
  adding
'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/Lib/lib/blas/fblas-
f2pywrappers.f'
to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'Lib/lib/blas/cblas.pyf.src' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'Lib/lib/lapack/clapack.pyf.src' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
  adding 'build/src.linux-x86_64-2.4/scipy/linalg/fblas.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
  adding
'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/scipy/linalg/fblas-
f2pywrappers.f'
to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.linux-x86_64-2.4/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.linalg.flapack" sources
  adding 'build/src.linux-x86_64-2.4/scipy/linalg/flapack.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
  adding
'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/scipy/linalg/flapack-
f2pywrappers.f'
to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.linux-x86_64-2.4/scipy/linalg/clapack.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.linalg.atlas_version" sources
building extension "scipy.linalg._iterative" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.linsolve._zsuperlu" sources
building extension "scipy.linsolve._dsuperlu" sources
building extension "scipy.linsolve._csuperlu" sources
building extension "scipy.linsolve._ssuperlu" sources
building extension "scipy.linsolve.umfpack.__umfpack" sources
  adding 'Lib/linsolve/umfpack/umfpack.i' to sources.
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.sparsetools" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.4' to include_dirs.
  adding 'build/src.linux-x86_64-2.4/Lib/stats/mvn-f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building data_files sources
running build_py
copying build/src.linux-x86_64-2.4/scipy/__config__.py ->
build/lib.linux-x86_64-2.4/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using build_ext
running install_lib
copying build/lib.linux-x86_64-2.4/scipy/__config__.py ->
/usr/lib64/python2.4/site-packages/scipy
byte-compiling /usr/lib64/python2.4/site-packages/scipy/__config__.py to
__config__.pyc
running install_data









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