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

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Tue Nov 16 21:25:01 EST 2004

There *is* a Windows installer for Biopython 1.30, for some reason it is not 
visible now on the Biopython website. I have updated the biopython webpage in 
CVS, but I cannot find the setup.py on the biopython webserver to install the 
new webpage. Does anybody know what happened with this setup.py?


Peter wrote:
> 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:
> http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial001.html#sec:windows_install
> 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
> 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"' 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
> Peter

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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