[BioC] Fwd: RCytoscape couldn't connect to host
Paul Shannon
pshannon at fhcrc.org
Fri Apr 27 19:05:40 CEST 2012
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
>
>
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