[Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu

Michiel de Hoon mdehoon at c2b2.columbia.edu
Sun Apr 29 05:33:33 UTC 2007

Sorry for my late reply.

Sebastian Bassi wrote:
> I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
> all dependencies and then I did:
> python setup.py build and it failed. So the second try was with N in
> the question about compiling Bio.KDTree and I got the same:

 From your output, Bio.KDTree does not seem to be the problem.

> sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
> running build
> running build_py
 > ...
> running build_ext
> building 'Bio.clistfns' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
> -Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
> Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
> In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
>                  from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
>                  from /usr/include/python2.4/Python.h:18,
>                  from Bio/clistfnsmodule.c:10:
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
> limits.h: No such file or directory
> In file included from Bio/clistfnsmodule.c:10:
> /usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory

If gcc cannot find standard headers such as limits.h or stdio.h, there 
seems to be a real problem with your installation. Can you compile a 
simple program with gcc if it #includes stdio.h? If not, try to solve 
that problem first. If so, try to find out why "gcc yourtestprogram.c" 
compiles, but "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall 
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c 
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o" 
doesn't. It may be that you have C_INCLUDE_PATH #defined somewhere, 
messing up the search paths.


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