Thanks for the report, I will look into this. rsbml currently has a number
of issues (it doesn't even compile for me right now). I need to look into
it this weekend.

Michael


On Fri, Mar 16, 2012 at 9:16 AM, hettling <j.hettling@vu.nl> wrote:

> Dear all,
>
> I have some trouble with SBML export using the package 'rsbml'.
> The following example of saving a very simple model to file gives an
> error on my machine:
>
> require('rsbml')
>
> com<-new("Compartment",id="default_compartment",name="default_compartment",size=1)
> sp<-new("Species",id="s1",name="s1",compartment=com@id
> ,initialConcentration=10)
>
> re<-new("Reaction",id="r1",name="r1",kineticLaw=new("KineticLaw",math=as.expression(0)),reactants=list(new("SpeciesReference",species="s1",stoichiometry=1)))
>
> sbml_model<-new("Model",id="mymodel",name="mymodel",compartments=list(com),species=list(sp),reactions=list(re))
>
> sbml_doc<-new("SBML",level=as.integer(2),ver=as.integer(2),model=sbml_model)
> rsbml_write(sbml_doc, file="myfile.xml")
>
> The error occurs in creating the SBML object, the message is:
> Error in validObject(.Object) : invalid class "SBML" object: FALSE
>
> If the KineticLaw in the reaction is NULL, e.g.:
>
>
> re<-new("Reaction",id="r1",name="r1",reactants=list(new("SpeciesReference",species="s1",stoichiometry=1)))
>
> the SBML export works without throwing errors. Also, if I create a
> document with SBML Level 2, version 1 instead of Level 2, version 2 in
> the example above, the code runs without errors. However, then only the
> SBML header is written to file and nothing else.
>
> I went through the documentation and tried it with the example models as
> well, but I cannot find a solution. I hope I understood right how to
> create a document object from a model object.
>
> I installed rsbml via the bioconductor and have libSBML version 4.0.1
> (that's whats written in the generated SBML) on Linux with R 2.13.1.
>
>
> Does anybody know what could be the problem here?
>
> Many thanks in advance,
>
> Hannes Hettling
>
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