[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 01:21:11 EST 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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