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}}
>>
>>
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>
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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