Question: Error converting SBML to graph Object using R SBML
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gravatar for Michael Lawrence
6.4 years ago by
United States
Michael Lawrence11k wrote:
Should be fixed in release: 2.18.1 On Wed, Jul 31, 2013 at 6:17 AM, Steve Lianoglou <lianoglou.steve@gene.com>wrote: > 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<mailto:>> lawrence.michael@gene.com>> >> >> Date: Tue, 30 Jul 2013 11:20:04 -0700 >> To: Dan Tenenbaum <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>> >> Cc: robin philip <robin.philip@agios.com<mailto:robin.philip@agios.com>>, >> "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" < >> bioconductor@r-project.org<mailto:bioconductor@r-project.org>> >> >> 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>> <mailto:dtenenba@fhcrc.org>> wrote: >> On Mon, Jul 29, 2013 at 11:50 AM, Robin Philip <robin.philip@agios.com>> <mailto:robin.philip@agios.com>> 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 >> 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]]
network graph convert rsbml • 565 views
ADD COMMENTlink written 6.4 years ago by Michael Lawrence11k
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