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

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Tue Dec 7 03:00:12 EST 2004

Finally, I found out how to update the Biopython web page. On the download page, 
you will now find a Windows installer for Biopython 1.30 for Python versions 
2.2, 2.3, and 2.4. Sorry for the delay. Please let me know if there are any 


Michiel Jan Laurens de Hoon wrote:

> 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?
> --Michiel.
> 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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