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 in fortranobject.o "_PyExc_TypeError", referenced from: _fortran_call in fortranobject.o _array_from_pyobj in fortranobject.o "_PyExc_ValueError", referenced from: _array_from_pyobj in fortranobject.o "_PyImport_ImportModule", referenced from: _init_fftpack in _fftpackmodule.o "_PyMem_Free", referenced from: _fortran_dealloc in fortranobject.o "_PyModule_GetDict", referenced from: _init_fftpack in _fftpackmodule.o "_PyNumber_Int", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PyObject_GetAttrString", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_repr in fortranobject.o "_PyObject_Str", referenced from: _array_from_pyobj in fortranobject.o "_PyObject_Type", referenced from: _array_from_pyobj in fortranobject.o "_PySequence_Check", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PySequence_GetItem", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PyString_AsString", referenced from: _fortran_repr in fortranobject.o _array_from_pyobj in fortranobject.o "_PyString_ConcatAndDel", referenced from: _fortran_getattr in fortranobject.o "_PyString_FromFormat", referenced from: _fortran_repr in fortranobject.o "_PyString_FromString", referenced from: _init_fftpack in _fftpackmodule.o _fortran_repr in fortranobject.o _fortran_getattr in fortranobject.o "_PyType_IsSubtype", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _array_from_pyobj.constprop.2 in fortranobject.o _array_from_pyobj in fortranobject.o "_PyType_Type", referenced from: _init_fftpack in _fftpackmodule.o "_Py_BuildValue", 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 ... "_Py_FindMethod", referenced from: _fortran_getattr in fortranobject.o "_Py_InitModule4_64", referenced from: _init_fftpack in _fftpackmodule.o "__PyObject_New", referenced from: _PyFortranObject_New in fortranobject.o _PyFortranObject_NewAsAttr in fortranobject.o "__Py_NoneStruct", referenced from: _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 _f2py_rout__fftpack_dct3 in _fftpackmodule.o ... "_main", referenced from: start in crt1.10.5.o ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status 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 in fortranobject.o "_PyExc_TypeError", referenced from: _fortran_call in fortranobject.o _array_from_pyobj in fortranobject.o "_PyExc_ValueError", referenced from: _array_from_pyobj in fortranobject.o "_PyImport_ImportModule", referenced from: _init_fftpack in _fftpackmodule.o "_PyMem_Free", referenced from: _fortran_dealloc in fortranobject.o "_PyModule_GetDict", referenced from: _init_fftpack in _fftpackmodule.o "_PyNumber_Int", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PyObject_GetAttrString", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _init_fftpack in _fftpackmodule.o _fortran_repr in fortranobject.o "_PyObject_Str", referenced from: _array_from_pyobj in fortranobject.o "_PyObject_Type", referenced from: _array_from_pyobj in fortranobject.o "_PySequence_Check", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PySequence_GetItem", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o "_PyString_AsString", referenced from: _fortran_repr in fortranobject.o _array_from_pyobj in fortranobject.o "_PyString_ConcatAndDel", referenced from: _fortran_getattr in fortranobject.o "_PyString_FromFormat", referenced from: _fortran_repr in fortranobject.o "_PyString_FromString", referenced from: _init_fftpack in _fftpackmodule.o _fortran_repr in fortranobject.o _fortran_getattr in fortranobject.o "_PyType_IsSubtype", referenced from: _int_from_pyobj.part.0 in _fftpackmodule.o _array_from_pyobj.constprop.2 in fortranobject.o _array_from_pyobj in fortranobject.o "_PyType_Type", referenced from: _init_fftpack in _fftpackmodule.o "_Py_BuildValue", 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 ... "_Py_FindMethod", referenced from: _fortran_getattr in fortranobject.o "_Py_InitModule4_64", referenced from: _init_fftpack in _fftpackmodule.o "__PyObject_New", referenced from: _PyFortranObject_New in fortranobject.o _PyFortranObject_NewAsAttr in fortranobject.o "__Py_NoneStruct", referenced from: _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 _f2py_rout__fftpack_dct3 in _fftpackmodule.o ... "_main", referenced from: start in crt1.10.5.o ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status error: Command "/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" failed with exit status 1
