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

[Michiel Jan Laurens de Hoon]

Thanks. I have updated setup.py in CVS.

Metzidis Anthony wrote:

> Hi,
> Thanks for following up on the problem. 
> 
> Taking your advice, I started from the original setup.py from CVS, and
> removed lines 201-202 as you instructed.   The build completed
> successfully. 
> 
> Best,
> Tony 
> 
> -----Original Message-----
> From: Michiel Jan Laurens de Hoon [mailto:mdehoon at ims.u-tokyo.ac.jp] 
> Sent: Friday, January 21, 2005 6:24 AM
> To: Metzidis Anthony; Biopython mailing list
> Subject: Re: [BioPython] build errors. "recompile with -fPIC"
> Biopython1.30 and 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
>>
>> 
>>
>> 
>>
>> 
>>
>>
>>
>>
>>
> 
> ------------------------------------------------------------------------
> 
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> 
> 

-- 
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