On Wed, Oct 27, 2010 at 11:57 AM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> A very odd bug was reported to me this morning.  Maybe somebody on this
> list will have some insight?
>
> My hypothesis is far-fetched, but it seems to fit the evidence:  in some
> rare circumstances, messages to or from the R httpd help server get mingled
> in with the XMLRPC transmissions upon which RCytoscape depends.  The XMLRPC
> package, or the XML package upon which it depends, understandably balks when
> sent &nbsp; <font> <br> and <p>
>
>

Paul,

If you set:
options("help_type"="html")
and then search for help for a function, like so:
?ls
It will launch a page in a browser window and you can see what port the help
server is on.
When I do this, I get:
http://127.0.0.1:19535/library/base/html/ls.html

Then I quit R and do it again, and get:
http://127.0.0.1:23172/library/base/html/ls.html

So it appears that R chooses a new (random?) port each time.

It is possible that R could be trying to use the ports that RCytoscape wants
to use.

Can you ask the user to quit R and try again and see if the conflict recurs?
Dan

	[[alternative HTML version deleted]]

