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Sebastian Bassi | 1 Sep 2004 14:36

[BioPython] Installing Biopython, where is the Makefile?

Hello,

I am still working on trying to install Biopython on AMD64.
According to several post (and one on this list) I have to compile it 
with -fPIC option.
But I can't find the Makefile.in where I should put this option.
Would the Makefile under Bio/KDTree a good place to put it? But I can't 
find cflags there. I think that switching this parameter is the only 
thing that is holding me back from compiling Biopython under AMD64.

--

-- 
Best regards,

//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ   //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center -      \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
\=// E-mail: sbassi <at> genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

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Michiel Jan Laurens de Hoon | 2 Sep 2004 03:47
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Re: [BioPython] Installing Biopython, where is the Makefile?

Does this error appear with KDTree only, or do you get the same error with other 
extension modules also?

--Michiel.

> /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation
> R_X86_64_32 can not be used when making a shared object; recompile with
> -fPIC
> build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols:
> Bad value
> collect2: ld returned 1 exit status
> error: command 'g++' failed with exit status 1

Sebastian Bassi wrote:
> Hello,
> 
> I am still working on trying to install Biopython on AMD64.
> According to several post (and one on this list) I have to compile it 
> with -fPIC option.
> But I can't find the Makefile.in where I should put this option.
> Would the Makefile under Bio/KDTree a good place to put it? But I can't 
> find cflags there. I think that switching this parameter is the only 
> thing that is holding me back from compiling Biopython under AMD64.
> 

--

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
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David Lapointe | 2 Sep 2004 04:09
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Re: [BioPython] Installing Biopython, where is the Makefile?

I get this error at KDTree also with Suse 9.1 ( x86_64). That's where the 
install exits so I don't know about subsequent modules.

On Wednesday 01 September 2004 09:47 pm, Michiel Jan Laurens de Hoon wrote:
> Does this error appear with KDTree only, or do you get the same error with
> other extension modules also?
>
> --Michiel.
>
> > /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation
> > R_X86_64_32 can not be used when making a shared object; recompile with
> > -fPIC
> > build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols:
> > Bad value
> > collect2: ld returned 1 exit status
> > error: command 'g++' failed with exit status 1
>
> Sebastian Bassi wrote:
> > Hello,
> >
> > I am still working on trying to install Biopython on AMD64.
> > According to several post (and one on this list) I have to compile it
> > with -fPIC option.
> > But I can't find the Makefile.in where I should put this option.
> > Would the Makefile under Bio/KDTree a good place to put it? But I can't
> > find cflags there. I think that switching this parameter is the only
> > thing that is holding me back from compiling Biopython under AMD64.

--

-- 
 .david
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Michiel Jan Laurens de Hoon | 2 Sep 2004 04:28
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Re: [BioPython] Installing Biopython, where is the Makefile?

I just tried to compile Biopython on my computer. KDTree is actually one of the 
last extension modules to be compiled; several others (for example Bio.Cluster) 
are compiled before setup.py reaches KDTree. Did any errors or warnings appear 
for the extension modules that are compiled before KDTree?

David Lapointe wrote:

> I get this error at KDTree also with Suse 9.1 ( x86_64). That's where the 
> install exits so I don't know about subsequent modules.
> 
> 
> On Wednesday 01 September 2004 09:47 pm, Michiel Jan Laurens de Hoon wrote:
> 
>>Does this error appear with KDTree only, or do you get the same error with
>>other extension modules also?
>>
>>--Michiel.
>>
>>
>>>/usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation
>>>R_X86_64_32 can not be used when making a shared object; recompile with
>>>-fPIC
>>>build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols:
>>>Bad value
>>>collect2: ld returned 1 exit status
>>>error: command 'g++' failed with exit status 1
>>
>>Sebastian Bassi wrote:
>>
>>>Hello,
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Sebastian Bassi | 2 Sep 2004 06:49

Re: [BioPython] Installing Biopython, where is the Makefile?

> I just tried to compile Biopython on my computer. KDTree is actually one
> of the
> last extension modules to be compiled; several others (for example
> Bio.Cluster)
> are compiled before setup.py reaches KDTree. Did any errors or warnings
> appear
> for the extension modules that are compiled before KDTree?

I am at the hotel now, tomorrow I will check it back in my workplace.
I THINK (NOT SURE!!) there were more complains like this and I got only
the last one for the sake of not sending to much program output to the
list.
Just to get the job done, I cp the /bio and /biodb tree from a working
installation (32bits) to this AMD64 computer, and IT WORKED!!! (thanks AMD
for making it backward compatible with i686!). It is not the best
solution, but at least could make the server work (I had several programs
wroten who depends on Biopython).
Anyway I will check this tomorrow morning.
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Sebastian Bassi | 2 Sep 2004 06:53

Re: [BioPython] Another problem with Biopython compilation on AMD64

> Ok my interest is piqued.  I'm not at work so I'll have to try this later
> but
> in the python documentation there is this gem.
> http://python.org/doc/current/inst/tweak-flags.html
> I can't find any files which would fit into this scheme.

I will see this tomorrow. Good piece
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Leighton Pritchard | 3 Sep 2004 16:47
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[BioPython] Job Opportunity - PhD, SCRI/BioSS Systems Biology


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Apologies for the broadcast, especially if this is not relevant to most
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Many thanks,

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Familiarity with scripting using Python or PERL would be helpful, plus
knowledge of methods for looking for patterns in molecular sequence data
(e.g. Hidden Markov models).  The work will involve the analysis of
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Iddo | 8 Sep 2004 19:50

Re: [BioPython] SwissProt parse error


Hey Mike,

Asa was using an old version of biopython, and that sorted itself out. 
However,  he was parsing a local file. Are you parsing a local or one 
you are reading from the ExPasy website?

Anyhow, if you email me a bare-bones version of your source code, I'll 
have a looksee.

Iddo

The problem then was that Asa was using an old version... but if you

Michael Sierk wrote:

> Hello, all,
>
> I'm getting the same error reported last year by Asa Ben Hur (  
> http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ).
> I just installed biopython a few weeks ago, and am a newbie with  
> python/biopython.  Any suggestions?
>
> Thanks,
> Mike Sierk
>
>> wrpmg4b:~ % python disulfides2.py test_seqs.aln
>> Swissprot ID:  Q14063
>> Traceback (most recent call last):
>>   File "disulfides2.py", line 73, in ?
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Michael Sierk | 8 Sep 2004 19:12
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[BioPython] SwissProt parse error

Hello, all,

I'm getting the same error reported last year by Asa Ben Hur (  
http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ).
I just installed biopython a few weeks ago, and am a newbie with  
python/biopython.  Any suggestions?

Thanks,
Mike Sierk

> wrpmg4b:~ % python disulfides2.py test_seqs.aln
> Swissprot ID:  Q14063
> Traceback (most recent call last):
>   File "disulfides2.py", line 73, in ?
>     seq_record = get_sprot_entry_remote(seq_id)
>   File "disulfides2.py", line 26, in get_sprot_entry_remote
>     entry = iterator.next()
>   File  
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next
>     return self._parser.parse(File.StringHandle(data))
>   File  
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse
>     self._scanner.feed(handle, self._consumer)
>   File  
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed
>     self._scan_record(uhandle, consumer)
>   File
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