[SciPy-Dev] Compiling scipy on macOS with conda environment
Andrew Nelson
andyfaff at gmail.com
Tue Aug 14 19:53:08 EDT 2018
Hi all,
I've been having issues compiling scipy/master on macOS in a Python 3.6
conda based environment (numpy 1.15).
I'm getting a whole load of undefined symbols, and the tail end of the
build log is below.
I've managed to get around the problem by setting LDFLAGS (based on
https://groups.google.com/a/continuum.io/forum/#!topic/conda/cwqTbwQAyW0):
export LDFLAGS="$LDFLAGS -undefined dynamic_lookup -bundle"
I have no idea why this works. Not sure why the problem comes about, but I
thought people might be interested in knowing what the solution could be.
/usr/local/bin/gfortran -Wall -g -Wl,-pie -Wl,-headerpad_max_install_names
-Wl,-dead_strip_dylibs
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/_fftpackmodule.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/drfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zrfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zfftnd.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/src/dct.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/src/dst.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/fortranobject.o
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../..
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../..
-Lbuild/temp.macosx-10.9-x86_64-3.6 -ldfftpack -lfftpack -lgfortran -o
build/lib.macosx-10.9-x86_64-3.6/scipy/fftpack/_
fftpack.cpython-36m-darwin.so
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o
...
"_PyBytes_FromString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyCapsule_GetPointer", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCapsule_New", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCapsule_Type", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_Type", referenced from:
_int_from_pyobj 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:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyErr_Format", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_call in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyErr_NewException", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyErr_NoMemory", referenced from:
_fortran_getattr in fortranobject.o
"_PyErr_Occurred", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
...
"_PyErr_Print", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_cfft in _fftpackmodule.o
_f2py_rout__fftpack_rfft in _fftpackmodule.o
...
"_PyExc_AttributeError", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyExc_RuntimeError", referenced from:
_PyInit__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
_check_and_fix_dimensions in fortranobject.o
"_PyImport_ImportModule", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyLong_AsLong", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
_fortran_getattr in fortranobject.o
"_PyMem_Malloc", referenced from:
_fortran_getattr in fortranobject.o
"_PyModule_Create2", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyModule_GetDict", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyNumber_Long", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyOS_snprintf", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GenericGetAttr", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GetAttrString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_int_from_pyobj in _fftpackmodule.o
_fortran_repr in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in _fftpackmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyUnicode_Concat", referenced from:
_fortran_getattr in fortranobject.o
"_PyUnicode_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyUnicode_FromString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyUnicode_FromStringAndSize", referenced from:
_fortran_getattr in fortranobject.o
"_Py_BuildValue", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o
...
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_cfft in _fftpackmodule.o
_f2py_rout__fftpack_rfft in _fftpackmodule.o
_f2py_rout__fftpack_crfft in _fftpackmodule.o
...
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o
...
"_PyBytes_FromString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyCapsule_GetPointer", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCapsule_New", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCapsule_Type", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_Type", referenced from:
_int_from_pyobj 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:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyErr_Format", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_call in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyErr_NewException", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyErr_NoMemory", referenced from:
_fortran_getattr in fortranobject.o
"_PyErr_Occurred", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
...
"_PyErr_Print", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_cfft in _fftpackmodule.o
_f2py_rout__fftpack_rfft in _fftpackmodule.o
...
"_PyExc_AttributeError", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyExc_RuntimeError", referenced from:
_PyInit__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
_check_and_fix_dimensions in fortranobject.o
"_PyImport_ImportModule", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyLong_AsLong", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
_fortran_getattr in fortranobject.o
"_PyMem_Malloc", referenced from:
_fortran_getattr in fortranobject.o
"_PyModule_Create2", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyModule_GetDict", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyNumber_Long", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyOS_snprintf", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GenericGetAttr", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GetAttrString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_int_from_pyobj in _fftpackmodule.o
_fortran_repr in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in _fftpackmodule.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in _fftpackmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_PyInit__fftpack in _fftpackmodule.o
"_PyUnicode_Concat", referenced from:
_fortran_getattr in fortranobject.o
"_PyUnicode_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyUnicode_FromString", referenced from:
_PyInit__fftpack in _fftpackmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyUnicode_FromStringAndSize", referenced from:
_fortran_getattr in fortranobject.o
"_Py_BuildValue", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfft_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_zfftnd_cache in _fftpackmodule.o
_f2py_rout__fftpack_destroy_drfft_cache in _fftpackmodule.o
...
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout__fftpack_zfft in _fftpackmodule.o
_f2py_rout__fftpack_drfft in _fftpackmodule.o
_f2py_rout__fftpack_zrfft in _fftpackmodule.o
_f2py_rout__fftpack_zfftnd in _fftpackmodule.o
_f2py_rout__fftpack_cfft in _fftpackmodule.o
_f2py_rout__fftpack_rfft in _fftpackmodule.o
_f2py_rout__fftpack_crfft in _fftpackmodule.o
...
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -Wl,-pie
-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/_fftpackmodule.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/drfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zrfft.o
build/temp.macosx-10.9-x86_64-3.6/scipy/fftpack/src/zfftnd.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/src/dct.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/src/dst.o
build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/scipy/fftpack/fortranobject.o
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../..
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../..
-Lbuild/temp.macosx-10.9-x86_64-3.6 -ldfftpack -lfftpack -lgfortran -o
build/lib.macosx-10.9-x86_64-3.6/scipy/fftpack/_
fftpack.cpython-36m-darwin.so" failed with exit status 1
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