On Tue, Feb 9, 2010 at 10:26 AM, Rainer Machne <raim@tbi.univie.ac.at>wrote:

>
> 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 :)
>
>
I think the latter solution would be best in the long term. The
configure.args argument *should* work with biocLite, so it would be good if
you pasted exactly what you were passing to the rsbml configure script.

Thanks,
Michael


> 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
>>
>> INSERM, U851
>> Marvel's Team "Immunité, Infection, Vaccination"
>> IFR128 (Biosciences Lyon Gerland)
>> 21, Av. Tony Garnier
>> 69007 LYON FRANCE
>>
>> Phone : + 33 (0)4 37 28 23 47
>> Fax : + 33 (0)4 37 28 23 41
>> Mail : stephane.schicklin@inserm.fr <mailto:stephane.schicklin@inserm.fr>
>
>
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