[BioPython] Compiling Bio.PDB.mmCIF.MMCIFlex on Windows

Peter biopython at maubp.freeserve.co.uk
Fri Feb 10 11:06:25 EST 2006


Michiel De Hoon wrote:
> You can use Cygwin to compile Biopython for Windows. That's how Biopython's
> installer for Windows is built. See
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python for some hints on
> how to build C extension modules for Windows using Cygwin.
> 
> --Michiel.

Your website is currently not responding, so I haven't been able to read 
it yet.

Does Cygwin cope with the Bio.PDB.mmCIF.MMCIFlex extension module?

I tried to compiled BioPython 1.41 with Python 2.3.3 on Windows XP SP2 
using MSVC 6.0 (Microsoft Visual C++ 6.0).

There is a problem with unistd.h missing while trying to compile file 
lex.yy.c into lex.yy.obj as shown below:

building 'Bio.PDB.mmCIF.MMCIFlex' extension
C:\Program Files\Microsoft Visual Studio\VC98\BIN\cl.exe /c /nologo /Ox 
/MD /W3
/GX /DNDEBUG -IBio -Ic:\python23\include -Ic:\python23\PC 
/TcBio/PDB/mmCIF/lex.yy.c 
/Fobuild\temp.win32-2.3\Release\Bio/PDB/mmCIF/lex.yy.obj
lex.yy.c
Bio/PDB/mmCIF/lex.yy.c(12) : fatal error C1083: Cannot open include 
file: 'unistd.h': No such file or directory
error: command '"C:\Program Files\Microsoft Visual 
Studio\VC98\BIN\cl.exe"' failed with exit status 2

Thank you

Peter



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