[SciPy-User] Installing SciPy on Mac OSX 10.6.5 - build errors with fftpack.so?

Rob Newman rlnewman@ucsd....
Mon Nov 29 18:23:08 CST 2010


Hi there SciPy gurus,

I am trying to install SciPy on my OSX machine. I have successfully installed Numpy and Matplotlib just fine, but am running into problems with SciPy. As per the SciPy website instructions, here is the information requested to help troubleshoot this. I searched the archives, but the posts seemed related to users having problems installing both packages, not just SciPy. It looks to me like the build fails at the g77 compile, possibly related to the library fftpack.so

Note that I have both Fortran g77 and GFortran installed just fine.

Thanks in advance for any help,
- Rob


OS Version: 10.6.5
Processor: 2.5 GHz Intel Core 2 Duo

GCC

hostname:scipy-0.8.0 rnewman$ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

GFORTRAN

hostname:scipy-0.8.0 rnewman$ gfortran --version
GNU Fortran (GCC) 4.4.0 20090203 (experimental) [trunk revision 143897]
Copyright (C) 2008 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

OUTPUT OF SETUP.PY BUILD
(Note that I have my own custom install of Python)

hostname:scipy-0.8.0 rnewman$ /opt/antelope/4.11/local/bin/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 = ['-faltivec', '-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 = ['-faltivec']

umfpack_info:
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
  libraries umfpack not found in /sw/lib
/Library/Python/2.6/site-packages/numpy/distutils/system_info.py:459: 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_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" 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-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' 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-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/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-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/lib/blas/fblas-f2pywrappers.f' to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/lib/blas/cblas.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/lib/lapack/clapack.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/linalg/fblas.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/linalg/fblas-f2pywrappers.f' to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.linalg.flapack" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/linalg/flapack.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/linalg/flapack-f2pywrappers.f' to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.macosx-10.6-universal-2.6/scipy/linalg/clapack.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' 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-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._superlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources
building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' to sources.
building extension "scipy.sparse.sparsetools._csr" sources
building extension "scipy.sparse.sparsetools._csc" sources
building extension "scipy.sparse.sparsetools._coo" sources
building extension "scipy.sparse.sparsetools._bsr" sources
building extension "scipy.sparse.sparsetools._dia" sources
building extension "scipy.spatial.ckdtree" sources
building extension "scipy.spatial._distance_wrap" sources
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.special.orthogonal_eval" sources
building extension "scipy.special.lambertw" sources
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.stats.vonmises_cython" sources
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.macosx-10.6-universal-2.6/fortranobject.c' to sources.
  adding 'build/src.macosx-10.6-universal-2.6' to include_dirs.
  adding 'build/src.macosx-10.6-universal-2.6/scipy/stats/mvn-f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
copying scipy/version.py -> build/lib.macosx-10.6-universal-2.6/scipy
copying build/src.macosx-10.6-universal-2.6/scipy/__config__.py -> build/lib.macosx-10.6-universal-2.6/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Found executable /usr/local/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
extending extension 'scipy.sparse.linalg.dsolve._superlu' defined_macros with [('USE_VENDOR_BLAS', 1)]
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using build_ext
building 'scipy.fftpack._fftpack' extension
compiling C sources
C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe

compile options: '-Iscipy/fftpack/src -Ibuild/src.macosx-10.6-universal-2.6 -I/Library/Python/2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c'
/usr/local/bin/g77 -g -Wall -g -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/src/dct.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0 -Lbuild/temp.macosx-10.6-universal-2.6 -ldfftpack -lfftpack -lg2c -lcc_dynamic -o build/lib.macosx-10.6-universal-2.6/scipy/fftpack/_fftpack.so
ld: library not found for -lcc_dynamic
collect2: ld returned 1 exit status
ld: library not found for -lcc_dynamic
collect2: ld returned 1 exit status
error: Command "/usr/local/bin/g77 -g -Wall -g -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-universal-2.6/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/scipy/fftpack/src/dct.o build/temp.macosx-10.6-universal-2.6/build/src.macosx-10.6-universal-2.6/fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0 -Lbuild/temp.macosx-10.6-universal-2.6 -ldfftpack -lfftpack -lg2c -lcc_dynamic -o build/lib.macosx-10.6-universal-2.6/scipy/fftpack/_fftpack.so" failed with exit status 1

ADDITIONAL INFO
Here is a simple test script that shows that both Numpy and Matplotlib are installed and working just fine against my custom install of Python:

#!/opt/antelope/4.11/local/bin/python

import sys 
import os

import numpy as np
print 'Numpy version: '+np.__version__

import matplotlib as mpl 
print 'Matplotlib version: '+mpl.__version__

And the output:

hostname: rnewman$ ./test.py 
Numpy version: 1.5.0
Matplotlib version: 1.0.0




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