rsbml: problem writing a model to file
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@michael-lawrence-3846
Last seen 2.3 years ago
United States
The translator should now be robust to "(". Of course, the document is not semantically valid, but it doesn't crash. Michael On Thu, Mar 22, 2012 at 12:33 PM, Michael Lawrence <michafla@gene.com>wrote: > > > 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",ma th=as.expression(parse(text="(A)"))),reactants=list(new("SpeciesRefere nce",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_compa rtment",size=1) >> > > >> > sp<-new("Species",id="s1",name="s1",compartment=com@id >> ,initialConcentration=10) >> > > >> > >> re<-new("Reaction",id="r1",name="r1",kineticLaw=new("KineticLaw",ma th=as.expression(0)),reactants=list(new("SpeciesReference",species="s1 ",stoichiometry=1))) >> > > >> > >> sbml_model<-new("Model",id="mymodel",name="mymodel",compartments=li st(com),species=list(sp),reactions=list(re)) >> > > >> > >> sbml_doc<-new("SBML",level=as.integer(2),ver=as.integer(2),model=sb ml_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("SpeciesRef erence",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]]
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