[SciPy-user] problems installing scipy on a mac.

Ashish Rastogi ashish.rastogi@gmail....
Thu Apr 23 16:35:18 CDT 2009


Hi all,

I am trying to install scipy and getting a strange error on my Mac. I  
have installed all the prerequisites, including FFTW and gfortran,  
Xcode tools and numpy. I am including the output that I receive,

Any help is much appreciated.

Thanks,
Ashish


dhcp-172-26-76-239:scipy$ python setup.py build
Warning: No configuration returned, assuming unavailable.
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
   libraries umfpack not found in /sw/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 "fftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" 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 "sc_c_misc" sources
building library "sc_cephes" sources
building library "sc_mach" sources
building library "sc_toms" sources
building library "sc_amos" sources
building library "sc_cdf" sources
building library "sc_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.integrate.dop" 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/src/ 
dfitpack-f2pywrappers.f' to sources.
building extension "scipy.interpolate._interpolate" 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.optimize._nnls" 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
conv_template:> build/src.macosx-10.5-i386-2.5/scipy/signal/lfilter.inc
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_src.py", line 87, in run
     self.build_sources()
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/command/build_src.py", line 106, in  
build_sources
     self.build_extension_sources(ext)
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/command/build_src.py", line 214, in  
build_extension_sources
     sources = self.template_sources(sources, ext)
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/command/build_src.py", line 322, in  
template_sources
     outstr = process_c_file(source)
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/conv_template.py", line 191, in  
process_file
     % (sourcefile, process_str(''.join(lines))))
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/conv_template.py", line 156, in  
process_str
     newstr[sub[0]:sub[1]], sub[4])
   File "/System/Library/Frameworks/Python.framework/Versions/2.5/ 
Extras/lib/python/numpy/distutils/conv_template.py", line 120, in  
expand_sub
     for k in range(numsubs):
TypeError: range() integer end argument expected, got NoneType.


dhcp-172-26-76-239:scipy$ python -c 'from numpy.f2py.diagnose import  
run; run()'
------
os.name='posix'
------
sys.platform='darwin'
------
sys.version:
2.5.1 (r251:54863, Jan 13 2009, 10:26:13)
[GCC 4.0.1 (Apple Inc. build 5465)]
------
sys.prefix:
/System/Library/Frameworks/Python.framework/Versions/2.5
------
sys.path=':/System/Library/Frameworks/Python.framework/Versions/2.5/ 
lib/python25.zip:/System/Library/Frameworks/Python.framework/Versions/ 
2.5/lib/python2.5:/System/Library/Frameworks/Python.framework/Versions/ 
2.5/lib/python2.5/plat-darwin:/System/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/plat-mac:/System/Library/ 
Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib- 
scriptpackages:/System/Library/Frameworks/Python.framework/Versions/ 
2.5/Extras/lib/python:/System/Library/Frameworks/Python.framework/ 
Versions/2.5/lib/python2.5/lib-tk:/System/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/lib-dynload:/Library/ 
Python/2.5/site-packages:/System/Library/Frameworks/Python.framework/ 
Versions/2.5/Extras/lib/python/PyObjC'
------
Failed to import Numeric: No module named Numeric
Failed to import numarray: No module named numarray
Found new numpy version '1.0.1' in /System/Library/Frameworks/ 
Python.framework/Versions/2.5/Extras/lib/python/numpy/__init__.pyc
Found f2py2e version '2_3473' in /System/Library/Frameworks/ 
Python.framework/Versions/2.5/Extras/lib/python/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in '/System/Library/Frameworks/ 
Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/ 
__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
customize CompaqFCompiler
customize NoneFCompiler
customize AbsoftFCompiler
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
customize IntelFCompiler
Could not locate executable f77
Could not locate executable f95
customize GnuFCompiler
customize SunFCompiler
customize NAGFCompiler
customize VastFCompiler
customize GnuFCompiler
customize IbmFCompiler
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 IntelVisualFCompiler
customize G95FCompiler
customize IntelItaniumFCompiler
customize PGroupFCompiler
customize LaheyFCompiler
customize CompaqVisualFCompiler
customize MipsFCompiler
customize HPUXFCompiler
customize IntelItaniumVisualFCompiler
customize IntelEM64TFCompiler
List of available Fortran compilers:
   --fcompiler=gnu  GNU Fortran Compiler (3.4.0)
List of unavailable Fortran compilers:
   --fcompiler=absoft   Absoft Corp Fortran Compiler
   --fcompiler=compaq   Compaq Fortran Compiler
   --fcompiler=compaqv  DIGITAL|Compaq Visual Fortran Compiler
   --fcompiler=g95      G95 Fortran Compiler
   --fcompiler=gnu95    GNU 95 Fortran Compiler
   --fcompiler=hpux     HP Fortran 90 Compiler
   --fcompiler=ibm      IBM XL Fortran Compiler
   --fcompiler=intel    Intel Fortran Compiler for 32-bit apps
   --fcompiler=intele   Intel Fortran Compiler for Itanium apps
   --fcompiler=intelem  Intel Fortran Compiler for EM64T-based apps
   --fcompiler=intelev  Intel Visual Fortran Compiler for Itanium apps
   --fcompiler=intelv   Intel Visual Fortran Compiler for 32-bit apps
   --fcompiler=lahey    Lahey/Fujitsu Fortran 95 Compiler
   --fcompiler=mips     MIPSpro Fortran Compiler
   --fcompiler=nag      NAGWare Fortran 95 Compiler
   --fcompiler=none     Fake Fortran compiler
   --fcompiler=pg       Portland Group Fortran Compiler
   --fcompiler=sun      Sun|Forte Fortran 95 Compiler
   --fcompiler=vast     Pacific-Sierra Research Fortran 90 Compiler
List of unimplemented Fortran compilers:
   --fcompiler=f  Fortran Company/NAG F Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing numpy.distutils.cpuinfo ... ok
------
CPU information: getNCPUs is_32bit is_i386 ------

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