[Biopython-dev] _pwm.c

Dragoslav Zaric zaricdragoslav at gmail.com
Thu Oct 28 14:16:34 UTC 2010

Dear Peter,

I wrote you this yesterday:

I put this in setup.py:

class build_ext_biopython(build_ext):
   def run(self):
       if not check_dependencies_once():
       # add software that requires NumPy to install
       # TODO - Convert these for Python 3
       if is_Numpy_installed():
           import numpy
           numpy_include_dir = numpy.get_include()
           #    Extension('Bio.Cluster.cluster',
           #              ['Bio/Cluster/clustermodule.c',
           #               'Bio/Cluster/cluster.c'],
           #              include_dirs=[numpy_include_dir],
           #              ))
           #    Extension('Bio.KDTree._CKDTree',
           #              ["Bio/KDTree/KDTree.c",
           #               "Bio/KDTree/KDTreemodule.c"],
           #              include_dirs=[numpy_include_dir],
           #              ))

and than I run:

python3.1 setup.py build_ext

This is output:

Biopython does not yet officially support Python 3, but you
can try it by first using the 2to3 script on our source code.
For details on how to use 2to3 with Biopython see README.
If you still haven't applied 2to3 to Biopython please abort now.
Do you want to continue this installation? (y/N):
running build_ext
building 'Bio.Motif._pwm' extension
creating build/temp.linux-i686-3.1
creating build/temp.linux-i686-3.1/Bio
creating build/temp.linux-i686-3.1/Bio/Motif
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
-I/usr/local/include/python3.1 -c Bio/Motif/_pwm.c -o
Bio/Motif/_pwm.c: In function ‘init_pwm’:
Bio/Motif/_pwm.c:123: warning: ‘return’ with a value, in function returning void
Bio/Motif/_pwm.c:125: warning: implicit declaration of function ‘Py_InitModule4’
Bio/Motif/_pwm.c:129: warning: assignment makes pointer from integer
without a cast
gcc -pthread -shared build/temp.linux-i686-3.1/Bio/Motif/_pwm.o -o

So as you can see this is compiling, but there are some warnings. So what is
plan, to compile totally without warnings ??


Dragoslav Zaric

Professional Programmer
MSc Astrophysics

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