[SciPy-dev] Error building from svn on Intel Macs.
Viral Shah
vshah at interactivesupercomputing.com
Sat May 31 15:54:36 EDT 2008
Attaching full output.
$ python setup.py build
Warning: No configuration returned, assuming unavailable.
mkl_info:
libraries mkl,vml,guide not found in /System/Library/Frameworks/
Python.framework/Versions/2.5/lib
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 /System/Library/Frameworks/
Python.framework/Versions/2.5/lib
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 /System/Library/Frameworks/
Python.framework/Versions/2.5/lib
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 /System/Library/Frameworks/
Python.framework/Versions/2.5/lib
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
blas_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/
vecLib.framework/Headers']
lapack_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3']
umfpack_info:
libraries umfpack not found in /System/Library/Frameworks/
Python.framework/Versions/2.5/lib
libraries umfpack not found in /usr/local/lib
libraries umfpack not found in /usr/lib
/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/
python/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
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 "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack" 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.cluster._hierarchy_wrap" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' 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.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/scipy/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.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources.
building extension "scipy.lib.blas.cblas" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/blas/cblas.pyf' to
sources.
f2py options: ['skip:', ':']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/lapack/
clapack.pyf' to sources.
f2py options: ['skip:', ':']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/fblas.pyf' to
sources.
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg.cblas" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/cblas.pyf' to
sources.
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.linalg.flapack" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/flapack.pyf' to
sources.
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources.
building extension "scipy.linalg.clapack" sources
adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/clapack.pyf' to
sources.
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.linalg.atlas_version" 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.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._zsuperlu" sources
building extension "scipy.sparse.linalg.dsolve._dsuperlu" sources
building extension "scipy.sparse.linalg.dsolve._csuperlu" sources
building extension "scipy.sparse.linalg.dsolve._ssuperlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack"
sources
building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' to
sources.
building extension "scipy.sparse.sparsetools._csr" sources
building extension "scipy.sparse.sparsetools._csc" sources
building extension "scipy.sparse.sparsetools._coo" sources
building extension "scipy.sparse.sparsetools._bsr" sources
building extension "scipy.sparse.sparsetools._dia" sources
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.stats.futil" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/scipy/stats/mvn-
f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building extension "scipy.ndimage._segment" sources
building extension "scipy.ndimage._register" sources
building extension "scipy.stsci.convolve._correlate" sources
building extension "scipy.stsci.convolve._lineshape" sources
building extension "scipy.stsci.image._combine" sources
building data_files sources
running build_py
copying scipy/__svn_version__.py -> build/lib.macosx-10.5-i386-2.5/scipy
copying build/src.macosx-10.5-i386-2.5/scipy/__config__.py -> build/
lib.macosx-10.5-i386-2.5/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize NAGFCompiler
customize AbsoftFCompiler
customize IbmFCompiler
Could not locate executable g77
Could not locate executable f77
Could not locate executable f95
customize GnuFCompiler
customize Gnu95FCompiler
Couldn't match compiler version for 'GNU Fortran (GCC)
4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU
Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou
may redistribute copies of GNU Fortran\nunder the terms of the GNU
General Public License.\nFor more information about these matters, see
the file named COPYING\n'
customize G95FCompiler
customize GnuFCompiler
customize Gnu95FCompiler
Couldn't match compiler version for 'GNU Fortran (GCC)
4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU
Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou
may redistribute copies of GNU Fortran\nunder the terms of the GNU
General Public License.\nFor more information about these matters, see
the file named COPYING\n'
customize NAGFCompiler
customize NAGFCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
customize AbsoftFCompiler
customize IbmFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
Couldn't match compiler version for 'GNU Fortran (GCC)
4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU
Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou
may redistribute copies of GNU Fortran\nunder the terms of the GNU
General Public License.\nFor more information about these matters, see
the file named COPYING\n'
customize G95FCompiler
customize GnuFCompiler
customize Gnu95FCompiler
Couldn't match compiler version for 'GNU Fortran (GCC)
4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU
Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou
may redistribute copies of GNU Fortran\nunder the terms of the GNU
General Public License.\nFor more information about these matters, see
the file named COPYING\n'
warning: build_ext: fcompiler=nag is not available.
building 'scipy.fftpack._fftpack' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -
mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall -DMACOSX -I/
usr/include/ffi -DENABLE_DTRACE -arch i386 -arch ppc -pipe
compile options: '-Ibuild/src.macosx-10.5-i386-2.5 -I/System/Library/
Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/
include -I/System/Library/Frameworks/Python.framework/Versions/2.5/
include/python2.5 -c'
Traceback (most recent call last):
File "setup.py", line 92, in <module>
setup_package()
File "setup.py", line 84, in setup_package
configuration=configuration )
File "/System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/numpy/distutils/core.py", line 174, in setup
return old_setup(**new_attr)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/command/build.py", line 112, in run
self.run_command(cmd_name)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/numpy/distutils/command/build_ext.py", line 121, in
run
self.build_extensions()
File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/command/build_ext.py", line 416, in build_extensions
self.build_extension(ext)
File "/System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/numpy/distutils/command/build_ext.py", line 312, in
build_extension
link = self.fcompiler.link_shared_object
AttributeError: 'NoneType' object has no attribute 'link_shared_object'
> On Fri, May 30, 2008 at 3:53 PM, Viral Shah
> <vshah at interactivesupercomputing.com> wrote:
>> I am using an Intel Mac, and trying to build scipy following the
>> instructions at: http://www.scipy.org/Installing_SciPy/Mac_OS_X
>>
>> I was able to successfully build numpy (from svn) without any extra
>> configuration. For scipy, even though I have installed the gfortran
>> compiler, setup doesn't seem to like the fact that I have 4.2.3. I am
>> using gcc 4.0.1 that is supplied by Apple. I get the following:
>>
>> customize G95FCompiler
>> customize GnuFCompiler
>> customize Gnu95FCompiler
>> Couldn't match compiler version for 'GNU Fortran (GCC)
>> 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU
>> Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou
>> may redistribute copies of GNU Fortran\nunder the terms of the GNU
>> General Public License.\nFor more information about these matters,
>> see
>> the file named COPYING\n'
>>
>> After searching around on scipy-dev, I resorted to doing this:
>>
>> $ python setup.py config_fc --fcompiler=gnu95 build
>>
>> That allowed me to get further, but left me with the following error
>> that I don't understand. I can help update the instructions page with
>> info about compilers, if I can get this process working. Thanks in
>> advance.
>
> Please provide the full output. The error that you see is a result of
> a failure to correctly configure the Fortran compiler earlier. The
> current numpy SVN should be able to handle the version string you give
> above.
>
>
> In [37]: from numpy.distutils.fcompiler import gnu
>
> In [38]: fc = gnu.Gnu95FCompiler()
>
> In [39]: v = 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free
> Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to
> the extent permitted by law.\nYou may redistribute copies of GNU
> Fortran\nunder the terms of the GNU General Public License.\nFor more
> information about these matters, see the file named COPYING\n'
>
> In [40]: print v
> GNU Fortran (GCC) 4.2.3
> Copyright (C) 2007 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
>
>
> In [41]: fc.version_match(v)
> Out[41]: '4.2.3'
>
> --
> 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
More information about the SciPy-Dev
mailing list