On Thu, Mar 22, 2012 at 11:28 AM, hettling <j.hettling@vu.nl> wrote:

> I found another small problem with writing my model to file:
> Whenever there are any parentheses in the math expression in a
> KineticLaw, the <kineticLaw/> tag in the written SBML file is empty.
>
> Even for a very simple reaction like:
>
>
> re<-new("Reaction",id="r1",name="r1",kineticLaw=new("KineticLaw",math=as.expression(parse(text="(A)"))),reactants=list(new("SpeciesReference",species="s1",stoichiometry=1)))
>
> I checked my document object within the "rsbml_write" and "rsbml_xml"
> functions and the math expression is correct there. I wrote a small C
> program to try if the writeSBML function in libsbml can even handle
> parentheses, and it does. In the io.c file, the generic libSBML
> functions are called..
>
> Therefore I suspect that something goes wrong in in creating the
> SBMLDocument c-object (in the doc.c file?)... do you think this is a god
> place to look?
>
> I do not want to bug you with requests all the time, and I will look
> further into it, it would be great if you could tell me if I am
> searching in the right place. After all I do not have experience with
> the R-to-C interface and find it quite hard to dubug.
>
>
The bug is probably in the conversion of the R language object to the AST
of the MathML. I'll need to find some time to dig into that one.

Michael


> Many thanks,
>
> Hannes
>
>
>
> On Thu, 2012-03-22 at 07:06 -0700, Michael Lawrence wrote:
> >
> >
> > On Wed, Mar 21, 2012 at 11:11 AM, hettling <j.hettling@vu.nl> wrote:
> >         Dear Michael,
> >
> >         Thanks a lot for your help! I got it to work with the
> >         development
> >         version of the package and libsbml 5.
> >
> >         The package does not compile anymore with libsbml 4; I guess
> >         the package
> >         uses the development version of SOSlib, which says it only
> >         works with
> >         libsbml 3.0.2 or the latest devel version, so it might be good
> >         to change
> >         the package requirements.
> >         I also had to downgrade sundials from 2.4.0 to 2.3.0 because
> >         of SOSlib.
> >
> >
> > Well, SOSlib is basically a dead library, and the package should still
> > compile, even if SOSlib fails to build. Of course, simulation support
> > would not be available.
> >
> >         Another thing is that the package gave an error creating an
> >         SBML
> >         document because it could not find the function
> >         "rsbml_perform_check",
> >         so I changed line 5 in SBML.R and set the variable "valid" to
> >         TRUE,
> >         which is a bit of a hack, but it works for now. Is this a
> >         check for the
> >         validity of the SBML document and is this check done with
> >         SOSlib?
> >
> >
> > I have fixed this. Not sure how that crept in.
> >
> > Thanks,
> > Michael
> >
> >         Many thanks,
> >
> >         Hannes
> >
> >
> >
> >
> >
> >         On Tue, 2012-03-20 at 18:03 -0700, Michael Lawrence wrote:
> >         > Well, it took a bit longer than I expected, but I have
> >         things now
> >         > working under libsbml 5.x. Should still work under 4.x
> >         (please let me
> >         > know).
> >         >
> >         > I have also fixed the validity checking that was causing
> >         your problem.
> >         > You'll need the devel (2.13.1) or wait for the release next
> >         month.
> >         >
> >         > Thanks,
> >         > Michael
> >         >
> >         > On Fri, Mar 16, 2012 at 10:27 AM, Michael Lawrence
> >         <michafla@gene.com>
> >         > wrote:
> >         >         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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> >         >                 Bioconductor@r-project.org
> >         >
> >         https://stat.ethz.ch/mailman/listinfo/bioconductor
> >         >                 Search the archives:
> >         >
> >
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >         >
> >         >
> >         >
> >
> >
> >
> >
>
>
>

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