I neglected to put my reply and Eleonaora's successful report back on the BioC list. Begin forwarded message: > From: "Eleonora Lusito" <eleonora.lusito at="" ifom-ieo-campus.it=""> > Subject: Re: RCytoscape couldn't connect to host > Date: April 27, 2012 9:41:02 AM PDT > To: "Paul Shannon" <paul.thurmond.shannon at="" gmail.com=""> > Cc: "Paul Shannon" <paul.thurmond.shannon at="" gmail.com="">,rcytoscape at googlegroups.com > > Dear Dott. Shannon, > finally it works very well!!!! Thank you ? The problem was on the plugin activation as you said. > > Best, > > Eleonora Lusito > > > > > > Paul Shannon (paul.thurmond.shannon at gmail.com) wrote: >> >> Dear Eleonora, >> >> I am glad you are giving RCytoscape a try. >> >> The usual cause of this problem you report is that >> >> 1) Cytoscape is not started (not the case here, I presume!) >> 2) Jan Bot's CytoscapeRPC plugin is not activated >> 3) That plugin is not configured to listen on port 9000 >> >> If you go to the Cytoscape Plugins menu, then mouse to CytoscapeRPC, you > will see a submenu like this: >> >> >> >> In my window, 'Activate ?' is grayed out indicating that the plugin is > active, and listening. >> >> What does your setup look like? >> >> Cheers! >> >> - Paul >> >> On Apr 27, 2012, at 8:04 AM, Eleonora Lusito wrote: >> >>> Dear Dott. Shannon, >>> I'm Eleonora Lusito, and I'm a PhD student in Computational Biology in > Milan. >>> I'm new in R, but I would like to use RCytoscape to plot networks. I >>> downloaded and installed Cytoscape (and the plug in CytoscapeRPC) and the >>> library RCytoscape. At the >>> same time I downloaded the XMLRPC and unzipped it (NB: all are in the >>> supported and suggested versions). The problem occurs during the >>> running of the example reported on the RCytoscape package pdf, that is: >>> library(RCytoscape) >>> g > g > g > g > cw > >>> after cw the following error message appears: >>> Error in function (type, msg, asError = TRUE) : couldn't connect to host. >>> >>> Can you help me please? >>> >>> Thanks in advance, >>> >>> Eleonora Lusito >>> >>> -- >>> Eleonora Lusito >>> Computational Biology PhD student >>> Molecular Medicine Program >>> via Ripamonti 435, 20141 Milano, Italy >>> >>> Phone number: +390294375160 >>> e-mail: eleonora.lusito at ifom-ieo-campus.it >>> >>> >> >> > > -- > Eleonora Lusito > Computational Biology PhD student > Molecular Medicine Program > via Ripamonti 435, 20141 Milano, Italy > > Phone number: +390294375160 > e-mail: eleonora.lusito at ifom-ieo-campus.it > >