[BioC] Fwd: RCytoscape couldn't connect to host

[Paul Shannon]

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
> 
>