[BioPython] build errors. "recompile with -fPIC" Biopython1.30and CVS, Python2.3, SuSE 9.1, AMD64 . Solution Found

[Lapointe, David]

This worked for me. I had the -fPIC problem with X86_64 before. This
works fine. I am testing 
now.

David 

> -----Original Message-----
> From: biopython-bounces at portal.open-bio.org 
> [mailto:biopython-bounces at portal.open-bio.org] On Behalf Of 
> Michiel Jan Laurens de Hoon
> Sent: Thursday, January 20, 2005 11:24 PM
> To: Metzidis Anthony; Biopython mailing list
> Subject: Re: [BioPython] build errors. "recompile with -fPIC" 
> Biopython1.30and CVS, Python2.3, SuSE 9.1, AMD64 . Solution Found
> 
> 
> Hi Metzidis,
> 
> Thanks for the patch. It seems though that removing the hacks 
> completely would 
> break compilation under Python 2.2, which is still supported 
> by Biopython. The 
> problem can be solved more easily by removing lines 201-202 
> in setup.py:
> 
>              elif build: # fix for 2.3, only if we are making 
> C++ modules
>                  self.compiler.compiler_so = 
> self.compiler.compiler_cxx
> 
> Could you try and see if that fixes the compilation problem 
> on your machine?
> 
> Compilation of KDTree is likely to be switched off by default 
> in future versions 
> of biopython because of recurring compilation problems on 
> various problems, but 
> it would be nice to fix setup.py as much as possible anyway 
> for people who want 
> to use it.
> 
> --Michiel.
> 
> 
> 
> Metzidis Anthony wrote:
> 
> > Hello everyone,
> > 
> >  
> > 
> > My Biopython (both version 1.30 and CVS) build failed with 
> the error 
> > "recompile with -fPIC"  on the file Bio/KDTree/KDTree.o.
> > 
> >  
> > 
> > I'm using BioPython CVS and 1.30, Python 2.3 on SuSE 9.1, AMD64.
> > 
> >  
> > 
> > I discovered that the problem was caused by some old hacks 
> in setup.py 
> > that altered the compilation of some c++ extensions.  Those 
> hacks were 
> > relevant to Python 2.2 (according to the documentation), but 
> > conflicted with python 2.3
> > 
> >  
> > 
> > The solution was to remove those 'hacks'.  After that, the build 
> > proceeded successfully.
> > 
> >  
> > 
> > I've attached a patch to the current CVS version of setup.py.  It 
> > seems to apply to biopython 1.30 as well.
> > 
> >  
> > 
> > Perhaps one of the developers could integrate the ideas in 
> the patch 
> > into the code.
> > 
> >  
> > 
> > Hope this helps someone!
> > 
> >  
> > 
> > Have a great day!
> > 
> >  
> > 
> > Best,
> > 
> > Tony
> > 
> >  
> > 
> >  
> > 
> >  
> > 
> > 
> > 
> > 
> > 
> ----------------------------------------------------------------------
> > --
> > 
> > _______________________________________________
> > BioPython mailing list  -  BioPython at biopython.org 
> > http://biopython.org/mailman/listinfo/biopython
> 
> -- 
> 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
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org 
> http://biopython.org/mailman/listinfo/biopytho> n
>