[BioC] rsbml: which libsbml version? (fwd)

[Rainer Machne]

On Tue, 9 Feb 2010, Stephane Schicklin wrote:

> Hi,
> I'm not using your library but I think your problem is different to a version 
> problem. If your libSBML is correctly installed, I advise you to search on 
> your system where really is the shared object "rsbml.so", then you'll have to 
> correct the path environment of R to have a correct load.
> ideas : is your system/R really 64 bits ? Look at 
> '/usr/lib*32*/R/library/rsbml/libs/rsbml.so' to see if your library is 
> compiled for 32 and not for 64 bits system...

Hi Stephane,
(sorry for the multiple emails, forgot the list in the first email)

thanks, but no, i think everything is 64bit and other libs are lying at the 
same location as rsbml. I found a potential source of the problem, though. I 
have a local installation of libsbml which I use outside of R. Even though the 
local installation is in my PATH and LD_LIBRARY_PATH variables, 
biocLite('rsbml') didn't find the headers and I didn't find out how to pass the 
local libsbml path to the biocLite installation scripts (? btw).

Thus i asked the sysadmin for a global libsbml installation. Installation of 
rsbml then worked fine, but ldd shows that the rsbml.so file then actually 
links to the local version:

merlin ~> ldd /usr/lib64/R/library/rsbml/libs/rsbml.so
...
libsbml.so => /MYLOCALLIBS/lib/libsbml.so
...

So, it seems to be a version conflict, which I often had with libsbml local vs. 
global installations. i should have though of ldd'ing the libs first.

I guess, I can try to remove the local installation temporarily from the path 
variables during rsbml installation to force it to use the global libsbml 
version, OR I could set the respective compilation flags via biocLite,if i find 
out how exactly (some tries with configure.args didn't work yet). I'll try 
tomorrow :)

Thanks,
Rainer


> Best wishes,
> 
> Stephane Schicklin
> 
> 
> Le 09/02/10 16:16, Rainer Machne a écrit :
>> Hi,
>> 
>> Which libSBML version is required for rsbml? I couldn't find this 
>> information anywhere, and it doesn't work for libSBML 3.4.1 (and 2.4.0) on 
>> Fedora Core 10 Linux.
>> 
>> Or is there another problem? Installation ended without error message, but 
>> then loading the library fails:
>> 
>> > library('rsbml',lib.loc="/usr/lib64/R/library/")
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared library '/usr/lib64/R/library/rsbml/libs/rsbml.so':
>>   /usr/lib64/R/library/rsbml/libs/rsbml.so: undefined symbol: 
>> SpeciesReferenceGlyph_getSpeciesReferenceId
>> Error : .onLoad failed in 'loadNamespace' for 'rsbml'
>> Error: package/namespace load failed for 'rsbml'
>> 
>> Thanks,
>> Rainer Machne
>> 
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> -- 
> Stéphane Schicklin
> Bioinformatics Engineer
> 
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