[Biopython-dev] [Bug 1733] compiler recognition in setup.py

[Michiel Jan Laurens de Hoon]

Compiling the two C++ modules Bio.KDTree and Bio.Affy has been a recurring 
problem for many Biopython users. From the KDTree source code, it seems that 
KDTree is implemented in C++ for the benefit of speed of the algorithms in 
KDTree.cpp. Can these routines be implemented in C or (better yet) using 
Numerical Python? Currently, Bio.KDTree is not included with the Windows 
installer either, because of compilation problems, and it would be nice to make 
this extension available to as many Biopython users as possible. On the other 
hand, compilation errors such as below may scare off new users, even if they are 
not planning to use Bio.KDTree and Bio.Affy, so it may be better to skip by 
default compilation of these extensions in setup.py. Thomas, any suggestions?

--Michiel.

bugzilla-daemon at portal.open-bio.org wrote:

> http://bugzilla.open-bio.org/show_bug.cgi?id=1733
> 
> 
> 
> 
> 
> ------- Additional Comments From MBatLE at gmx.de  2005-01-17 09:52 -------
> The consequence in that the 'Bio.KDTree._CKDTree' extension cant get build. 
> The relevant output of setup.py is:
> 
> building 'Bio.KDTree._CKDTree' extension
> creating build/temp.linux-i686-2.3/Bio/KDTree
> -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o
> build/temp.linux-i686-2.3/Bio/KDTree/KDTree.swig.o
> unable to execute -I/usr/include/python2.3: No such file or directory
> error: command '-I/usr/include/python2.3' failed with exit status 1
> 
> 
> 
> 
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-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon