Hi, On Tuesday, July 30, 2013, Robin Philip wrote: > Any ideas about the release date of version 2.19? It would be useful to me > since I am trying to standardise a few codes and eliminate dependency on > matlab for doing the same. It takes a day or two to push through the build system. Note that this is in the devel branch, though, > > From: Michael Lawrence <lawrence.michael@gene.com <javascript:;=""><mailto:> lawrence.michael@gene.com <javascript:;>>> > Date: Tue, 30 Jul 2013 11:20:04 -0700 > To: Dan Tenenbaum <dtenenba@fhcrc.org <javascript:;=""><mailto:> dtenenba@fhcrc.org <javascript:;>>> > Cc: robin philip <robin.philip@agios.com <javascript:;=""><mailto:> robin.philip@agios.com <javascript:;>>>, "bioconductor@r-project.org<javascript:;> > <mailto:bioconductor@r-project.org <javascript:;="">>" < > bioconductor@r-project.org <javascript:;><mailto:> bioconductor@r-project.org <javascript:;>>> > Subject: Re: [BioC] Error converting SBML to graph Object using R SBML > > Even without that information, it is pretty obvious that there are bugs in > the code. I was a total R newbie at that point. I managed to reproduce the > error with the curto.xml file in the package, and it's now fixed in devel, > version 2.19.1. I didn't realize that reactions could have zero reactants > or zero products. Must be source/sinks in the network. > > > > On Tue, Jul 30, 2013 at 10:06 AM, Dan Tenenbaum <dtenenba@fhcrc.org<javascript:;> > <mailto:dtenenba@fhcrc.org <javascript:;="">>> wrote: > On Mon, Jul 29, 2013 at 11:50 AM, Robin Philip <robin.philip@agios.com<javascript:;> > <mailto:robin.philip@agios.com <javascript:;="">>> wrote: > > Hello, > > > > I am trying to convert an SBML model to a graph object in R. > > The following are the commands I use to do so. > > > > > doc<-rsbml_read(system.file('sbml','RAW264_7_v2.xml',package='rsbml' ),dom=FALSE) > > g<-rsbml_graph(doc) > > > > I get the following error in the last line > > Error in gNodes[x$edges] : invalid subscript type 'list' > > > > Can someone suggest a remedy? > > > > > Please send the output of the sessionInfo() command. > I don't see the file RAW264_7_v2.xml in either the release or devel > version of rsbml. > > Dan > > > > Regards > > Robin Philip > > > > This message contains information which may be confide...{{dropped:28}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech [[alternative HTML version deleted]]