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scipy 0.12 installation error (building from source)

asked 2013-04-11 04:58:01 -0500

Dustin gravatar image

updated 2013-04-11 06:00:02 -0500

I am trying to install the newest stable version of scipy (which is 0.12) from the source into sage's python distribution, but I am getting a error in quite deep in the build process. The problem appears to be missing symbols in _fftpackmodule.o.

I am running Mac OS X 10.7.5 and Sage Version 5.8, Release Date: 2013-03-15.

I am performing the install by doing the following (I have successfully installed several other additional python modules this way):

sage -sh

cd scipy/source/folder/on/the/Desktop

python setup.py install

Here is the relevant errors:

/Applications/sage/local/bin/gfortran -Wall build/temp.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-x86_64-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-x86_64-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-x86_64-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-x86_64-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/scipy/fftpack/src/dst.o build/temp.macosx-10.6-x86_64-2.7/build/src.macosx-10.6-x86_64-2.7/fortranobject.o -L/Applications/sage/local/bin/../lib/gcc/x86_64-apple-darwin10.8.0/4.6.3 -Lbuild/temp.macosx-10.6-x86_64-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-x86_64-2.7/scipy/fftpack/_fftpack.so Undefined symbols for architecture x86_64: "_PyArg_ParseTupleAndKeywords", referenced from: _f2py_rout__fftpack_destroy_dst1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dst2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddst1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddst2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o ... "_PyCObject_AsVoidPtr", referenced from: _init_fftpack in _fftpackmodule.o _F2PyCapsule_AsVoidPtr in fortranobject.o "_PyCObject_FromVoidPtr", referenced from: _fortran_getattr in fortranobject.o _F2PyCapsule_FromVoidPtr in fortranobject.o "_PyCObject_Type", referenced from: _init_fftpack in _fftpackmodule.o _F2PyCapsule_Check in fortranobject.o "_PyComplex_Type", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PyDict_DelItemString", referenced from: _fortran_setattr in fortranobject.o "_PyDict_GetItemString", referenced from: _fortran_getattr in fortranobject.o "_PyDict_New", referenced from: _fortran_setattr in fortranobject.o _PyFortranObject_New in fortranobject.o _PyFortranObject_NewAsAttr in fortranobject.o "_PyDict_SetItemString", referenced from: _init_fftpack in _fftpackmodule.o _fortran_getattr in fortranobject.o _fortran_setattr in fortranobject.o _F2PyDict_SetItemString in fortranobject.o _PyFortranObject_New in fortranobject.o "_PyErr_Clear", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _fortran_repr in fortranobject.o _F2PyDict_SetItemString in fortranobject.o "_PyErr_Format", referenced from: _init_fftpack in _fftpackmodule.o _fortran_call in fortranobject.o "_PyErr_NewException", referenced from: _init_fftpack in _fftpackmodule.o "_PyErr_Occurred", referenced from: _f2py_rout__fftpack_destroy_dst1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dst2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddst1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddst2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_dct2_cache in _fftpackmodule.o _f2py_rout__fftpack_destroy_ddct1_cache in _fftpackmodule.o ... "_PyErr_Print", referenced from: _init_fftpack in _fftpackmodule.o _F2PyDict_SetItemString in fortranobject.o "_PyErr_SetString", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _f2py_rout__fftpack_dst3 in _fftpackmodule.o _f2py_rout__fftpack_dst2 in _fftpackmodule.o _f2py_rout__fftpack_dst1 in _fftpackmodule.o _f2py_rout__fftpack_ddst3 in _fftpackmodule.o _f2py_rout__fftpack_ddst2 in _fftpackmodule.o _f2py_rout__fftpack_ddst1 in _fftpackmodule.o ... "_PyExc_AttributeError", referenced from: _init_fftpack in _fftpackmodule.o _fortran_setattr in fortranobject.o "_PyExc_ImportError", referenced from: _init_fftpack in _fftpackmodule.o "_PyExc_RuntimeError", referenced from: _init_fftpack in _fftpackmodule.o _fortran_call ... (more)

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answered 2013-04-11 08:00:39 -0500

Version 0.11 of scipy is included in Sage. Based on its Sage-specific build file, in OS X I would try

sage -sh
unset CFLAGS CXXFLAGS SHAREDFLAGS
unset ATLAS BLAS LAPACK
export LDFLAGS="-bundle -undefined dynamic_lookup $LDFLAGS"
export FFLAGS="$FFLAGS -fPIC"
export FCFLAGS="$FCFLAGS -fPIC"
UMFPACK="None"; export UMFPACK
cd scipy/source/folder/on/the/Desktop
python setup.py install
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Comments

This worked! Thanks!

Dustin gravatar imageDustin ( 2013-04-12 04:37:01 -0500 )edit

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Asked: 2013-04-11 04:58:01 -0500

Seen: 713 times

Last updated: Apr 11 '13