[Biopython-dev] Building biopython 1.30 on Windows with MSCV

Peter peter at maubp.freeserve.co.uk
Tue Nov 16 12:48:08 EST 2004

I'm trying to build and/or install BioPython 1.30 on Windows XP.

I would guess that since there isn't a Windows installer for Biopython 1.30 (yet) that most development occurs on linux/unix.

Furthermore, the only instructions in the documentation are for Borland's free C++ compiler:


I have Microsoft Visual C++ 6.0 (MSVC) which I have successfully used to compile other python extensions (both a simple install, and creation of a windows installation program).

In theory using MSVC 6.0 should actually be easier, but it looks like no-one has tried this recently as there is a library problem of some sort.  If I try this for BioPython 1.30:

python setup.py bdist_wininst

After a few warnings, it fails here:

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
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"' fail
ed with exit status 2

Before I can too carried away, does anyone on the list have any experience of building BioPython on windows?

Thank you



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