[SciPy-dev] Error building from svn on Intel Macs.

Viral Shah vshah@interactivesupercomputing....
Sat May 31 14:54:36 CDT 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@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



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