[SciPy-User] Scipy build problem

Daniel Morton dacmorton@gmail....
Sun Feb 24 21:36:33 CST 2013


When I attempted to upgrade to the most recent version of scipy the build
failed with the following error message:

error: command 'swig' failed with exit status 1.

I have Mac OS X 10.6.8.

I have gcc version 4.2.1 and gfortran version 4.6.0. I don't know where I
got gfortran from.

I'm trying to install scipy 0.11.0 and have numpy 1.8.0.

The complete printout from the build follows:

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']

Running from scipy source directory.
umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include', '-I/usr/local/include']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands
--fcompiler options
running build_src
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_scipy" sources
building library "sc_c_misc" sources
building library "sc_cephes" sources
building library "sc_mach" 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-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' 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-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.integrate.lsoda" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.interpolate.interpnd" sources
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
  adding
'build/src.macosx-10.6-intel-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f'
to sources.
building extension "scipy.interpolate._interpolate" sources
building extension "scipy.io.matlab.streams" sources
building extension "scipy.io.matlab.mio_utils" sources
building extension "scipy.io.matlab.mio5_utils" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
  adding
'build/src.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/lib/blas/fblas-f2pywrappers.f'
to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'build/src.macosx-10.6-intel-2.7/scipy/lib/blas/cblas.pyf' to
sources.
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'build/src.macosx-10.6-intel-2.7/scipy/lib/lapack/clapack.pyf' to
sources.
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.linalg._fblas" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
  adding
'build/src.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/linalg/_fblas-f2pywrappers.f'
to sources.
building extension "scipy.linalg._flapack" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
  adding
'build/src.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/linalg/_flapack-f2pywrappers.f'
to sources.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
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-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal._spectral" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
  adding 'build/src.macosx-10.6-intel-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-intel-2.7' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._superlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources
  adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.
swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i
swig -python -I/usr/local/include -I/usr/local/include -I/usr/local/include
-o
build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c
-outdir build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack
scipy/sparse/linalg/dsolve/umfpack/umfpack.i
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:192: Error: Unable to find
'umfpack.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:193: Error: Unable to find
'umfpack_solve.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:194: Error: Unable to find
'umfpack_defaults.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:195: Error: Unable to find
'umfpack_triplet_to_col.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:196: Error: Unable to find
'umfpack_col_to_triplet.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:197: Error: Unable to find
'umfpack_transpose.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:198: Error: Unable to find
'umfpack_scale.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:200: Error: Unable to find
'umfpack_report_symbolic.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:201: Error: Unable to find
'umfpack_report_numeric.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:202: Error: Unable to find
'umfpack_report_info.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:203: Error: Unable to find
'umfpack_report_control.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:215: Error: Unable to find
'umfpack_symbolic.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:216: Error: Unable to find
'umfpack_numeric.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:225: Error: Unable to find
'umfpack_free_symbolic.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:226: Error: Unable to find
'umfpack_free_numeric.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:248: Error: Unable to find
'umfpack_get_lunz.h'
scipy/sparse/linalg/dsolve/umfpack/umfpack.i:272: Error: Unable to find
'umfpack_get_numeric.h'
error: command 'swig' failed with exit status 1
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