[Biopython-dev] Oligopython page

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Wed Apr 7 22:54:32 EDT 2004

I tried compiling KDTree on a Unix machine running SunOS 5.8. It has two Python 
versions, one compiled with gcc and the other one with the native cc compiler. 
Distutils uses the same compiler as the one used to compile Python itself. The 
gcc-Python compiled KDTree without problems, but the cc-Python did not, as cc 
doesn't handle C++. The same problem may occur on other Unix platforms if the 
native compiler rather than gcc was used to compile Python.


Thomas Hamelryck wrote:

> On Wednesday 07 April 2004 00:00, Brad Chapman wrote:
>>If I remember properly, the reason KDTree is not installed by
>>default isn't because it's C++ but rather because it used the C++
>>standard library (stdc++) which caused building problems on some
>>systems without development libraries.
> To quote from an older post:
> KDTree works fine. But: it needs a working C++ compiler, and 
> a complete installation of Numpy (including header files) to compile. 
> It seems that on Solaris it does not compile due to a bug in Distutils, which 
> is not really coping well with C++ on some platforms (ie. missing flags, 
> compiling with gcc instead of g++ etc.). 
> ---
> Thomas Hamelryck
> Bioinformatik centret      
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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

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