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

Ashish Rastogi ashish.rastogi@gmail....
Thu Apr 23 19:28:43 CDT 2009


An SVN revision. The version.py file under the scipy directory says 0.8.0
Thanks,
Ashish


On Thu, Apr 23, 2009 at 6:53 PM, David Warde-Farley <dwf@cs.toronto.edu>wrote:

> 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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> > SciPy-user@scipy.org
> > http://mail.scipy.org/mailman/listinfo/scipy-user
>
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