[SciPy-User] Fwd: segfault

Paul Anton Letnes paul.anton.letnes@gmail....
Sun Aug 14 15:56:34 CDT 2011


Replying to myself with a bit more information. I tried installing the most recent scipy from the git repository into a virtualenv, but I ran into problems with umfpack.
% python setup.py build
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']

non-existing path in 'scipy/io': 'docs'
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 /Users/paulanto/Desktop/Rayleigh2D-debug/dev-scipy/bin/../lib
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
amd_info:
  libraries amd not found in /Users/paulanto/Desktop/Rayleigh2D-debug/dev-scipy/bin/../lib
  libraries amd not found in /usr/local/lib
  libraries amd not found in /usr/lib
  FOUND:
    libraries = ['amd']
    library_dirs = ['/opt/local/lib']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/opt/local/lib']

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 "qhull" 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-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' 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-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' 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-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-2.7/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: ['skip:', ':']
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/lib/blas/fblas-f2pywrappers.f' to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'build/src.macosx-10.6-x86_64-2.7/scipy/lib/blas/cblas.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'build/src.macosx-10.6-x86_64-2.7/scipy/lib/lapack/clapack.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/linalg/fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.macosx-10.6-x86_64-2.7/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.linalg.flapack" sources
  adding 'build/src.macosx-10.6-x86_64-2.7/scipy/linalg/flapack.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
  adding 'build/src.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/linalg/flapack-f2pywrappers.f' to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.macosx-10.6-x86_64-2.7/scipy/linalg/clapack.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' 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-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
  adding 'build/src.macosx-10.6-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' 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-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-x86_64-2.7' 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 -o build/src.macosx-10.6-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.6-x86_64-2.7/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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