Re: RCytoscape couldn't connect to host

[Paul Shannon]

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 <- new ('graphNEL', edgemode='directed')
 g <- graph::addNode ('A', g)
 g <- graph::addNode ('B', g)
 g <- graph::addNode ('C', g)
 cw <- new.CytoscapeWindow ('vignette', graph=g)

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: eleonor...@ifom-ieo-campus.it