[BioPython] trying to install under cygwin

[Michiel Jan Laurens de Hoon]

Most likely you are mixing Windows and Cygwin here. Since python 
setup.py build tries to use the Visual C++ compiler, and includes files 
from Python for Windows, you are probably running Python for Windows 
instead of Cygwin's python. By using --compiler=cygwin, you force it to 
use Cygwin's gcc compiler, which then causes trouble.

I am not sure if you are trying to install biopython for Python for 
Windows or for Cygwin's python. In the first case, you can use mingw's 
compiler by running python setup.py build --compiler=mingw32. If you 
want to use Cygwin's python, then make sure it is actually installed in 
your cygwin and that it appears first in the path (so before 
/cygdrive/d/python22). You shouldn't have to specify --compiler=cygwin 
in either case.

--Michiel.

Daniel Rubin wrote:

> I'm trying to install the latest biopython in cvs
> under cygwin. But the python setup.py build command
> fails during the process when it tries to execute
> "cl.exe" and cannot find that command.
> 
> Next, I tried python setup.py build --compiler=cygwin
> and but then I get this error:
> 
> In file included from
> d:/ProgramFiles/python22/include/Python.h:62,
>                  from Bio/cSVMmodule.c:12:
> d:/ProgramFiles/python22/include/pyport.h:480:2:
> #error "LONG_BIT definition appears wrong for platf
> orm (bad gcc/glibc config?)."
> error: command 'gcc' failed with exit status 1
> 
> Any suggestions?
> 
> Daniel
> 
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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