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

David Warde-Farley dwf@cs.toronto....
Thu Apr 23 17:53:58 CDT 2009


Hi,

What version of SciPy are you trying to compile? 0.7.0 or an SVN  
revision?

David

On 23-Apr-09, at 5:35 PM, Ashish Rastogi wrote:

> 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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