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",mat h=as.expression(parse(text="(A)"))),reactants=list(new("SpeciesReferen ce",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_compar tment",size=1) > > > > > sp<-new("Species",id="s1",name="s1",compartment=com@id > ,initialConcentration=10) > > > > > > re<-new("Reaction",id="r1",name="r1",kineticLaw=new("KineticLaw",mat h=as.expression(0)),reactants=list(new("SpeciesReference",species="s1" ,stoichiometry=1))) > > > > > > sbml_model<-new("Model",id="mymodel",name="mymodel",compartments=lis t(com),species=list(sp),reactions=list(re)) > > > > > > sbml_doc<-new("SBML",level=as.integer(2),ver=as.integer(2),model=sbm l_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("SpeciesRefe rence",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 > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]]