Failure to build Cython module using distutils

Question

I am trying to build Cython to try to call C functions from python by trying to link cython with C headers. When I try to use this command to build python

python setup.py build_ext --inplace

it shows this error:

running build_ext
building 'cython' extension
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cython.c -o build/temp.macosx-10.6-intel-2.7/cython.o
cython.c:692:14: error: typedef redefinition with different types ('void' vs
      'struct _typeobject')
typedef void PyTypeObject;
             ^
/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/object.h:411:3: note: 
      previous definition is here
} PyTypeObject;
  ^
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1

Edit: my cython.pyx looks like this:

cdef extern from "rnafoldenergy.h":
    float dostuff(int maxw, char *sequence2, char *sequence3, float *freeenergy)



cpdef int dothings():
    print "Hello!"

    cdef int maxw = 50

    cdef float freeenergyarray[3]
    freeenergyarray[:] = [0, 0, 0]
    cdef char* sequence2 = "AAACATTGAAAATAAGAGTACATGAAGGATATGAGGAATTCACAATGGTTGGGCGAAGAGCAACAGCCATTCTAAGGAAAGCAACCAGAAGACTGATCCAACTGATAGTGAGTGGGAAAG"
    cdef char* sequence3 = "ATCCTTCATGTACTCTTATTTTCAATGTTTATAAAAGAGGAGAAATATAAAATGTGAAAATAAAACCTGGCGGCAGCGCAAAAG"

    cdef float interactenergy=0


    interactenergy=dostuff(maxw=maxw, sequence2=sequence2, sequence3=sequence3, freeenergy=freeenergyarray)


    print "A: %f, B: %f, AB: %f, Interact: %f" % (freeenergyarray[0],freeenergyarray[1],freeenergyarray[2],interactenergy)

    return 0

What's in cython.pyx? Without it this question is probably impossible to answer. — DavidW

DavidW DavidW · Accepted Answer · 2017-07-29T09:40:15

I think it's because you've calling your file "cython.pyx". I can reproduce your error with a file called "cython.pyx" but if I rename it to something else then I don't get the line typedef void PyTypeObject; and so don't get the error.

It's a bit of a mystery why this generates that exact error, but given there's already a module called "cython" (which you're using...) it seems a good idea not to call your module the same thing.

Failure to build Cython module using distutils

1 Answers