Can't connect to host

[Bill Raynor]

I am getting the previous reported "Can't connect to host" message on a corporate workstation.

R and Cytoscape work together just fine on

1. Personal macbook pro
2. personal windows 7 machine

but the combination fails on my work laptop, where I acutually need to use it. 

 

Setup:

I am running R 2.15.1 and Cytoscape 2.8.3 on a windows 7 enterprise machine, service pack 1, an I7 with 12 GB Ram and 256 GB SSD. I have installed and configured CytoscapeRPC, running using the default port 9000. I have also enabled the proxy in Cytoscape and am using the proxy library in R. I can telnet localhost 9000 (although Cytoscape does not respond).  R can talk to the internet (e.g. to source biocLite.r)

 

symptom:

when I run the sequence of commands R cannot connect to Cytoscape:

> library(igraph)

> library(XMLRPC)

> testResponse = xml.rpc('http://localhost:9000', 'Cytoscape.test')

Error in function (type, msg, asError = TRUE)  : couldn't connect to host

The same error occurs if I use the 'new.CytoscapeWindow(...)' sequence from the vignette.

 

What is causing this error, and how can I fix the machine?

 

Thanks

 

Further information: here's the trace info I get when I start Cytoscape.bat

cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization

cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu

cytoscape[INFO]: starting delete action

cytoscape[INFO]: ending delete action

cytoscape[INFO]: PreferenceAction()...

cytoscape.actions.BookmarkAction[INFO]: BookmarkAction()...

Loading CytoscapeRPCPlugin

com.sun.xml.internal.ws.wsdl.parser.InaccessibleWSDLException: 2 counts of InaccessibleWSDLException.

java.net.SocketException: Connection reset

java.net.SocketException: Connection reset

        at com.sun.xml.internal.ws.wsdl.parser.RuntimeWSDLParser.tryWithMex(Unknown Source)

        at com.sun.xml.internal.ws.wsdl.parser.RuntimeWSDLParser.parse(Unknown Source)

        at com.sun.xml.internal.ws.client.WSServiceDelegate.parseWSDL(Unknown Source)

        at com.sun.xml.internal.ws.client.WSServiceDelegate.<init>(Unknown Source)

        at com.sun.xml.internal.ws.client.WSServiceDelegate.<init>(Unknown Source)

        at com.sun.xml.internal.ws.spi.ProviderImpl.createServiceDelegate(Unknown Source)

        at javax.xml.ws.Service.<init>(Unknown Source)

        at gov.nih.nlm.ncbi.soap.eutils.EUtilsService.<init>(EUtilsService.java:46)

        at edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClient.<init>(NCBIClient.java:212)

        at edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClient.<clinit>(NCBIClient.java:185)

        at edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClientPlugin.<init>(NCBIClientPlugin.java:60)

        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)

        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)

        at java.lang.reflect.Constructor.newInstance(Unknown Source)

        at java.lang.Class.newInstance0(Unknown Source)

        at java.lang.Class.newInstance(Unknown Source)

        at cytoscape.plugin.CytoscapePlugin.loadPlugin(CytoscapePlugin.java:134)

        at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:993)

        at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:915)

        at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:837)

        at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:656)

        at cytoscape.CytoscapeInit.init(CytoscapeInit.java:209)

        at cytoscape.CyMain.<init>(CyMain.java:144)

        at cytoscape.CyMain.main(CyMain.java:108)

XML-RPC Port: 9000

 

 

 

 

[Paul Shannon]

Bill,

Your test of telnet-ing to localhost 9000 -- that it worked, but that Cytoscape did not respond -- may be our best clue here. In a possibly similar corporate situation a couple of years ago, we puzzled for a week over the problem and then got this solution:

The corporate firewall block loopback on localhost/127.0.0.1 from certain programs (I don't understand why only
certain programs are blocked). So i have to add exceptions to my firewall to allow loopback on '127.0.0.1'
for R.exe.

Maybe something similar is happening with you?

Here is another test, though it may get you no further than telnet did:

shell> python
>>> import xmlrpclib
>>> server = xmlrpclib.ServerProxy("http://localhost:9000")
>>> print server.Cytoscape.test()
It works!

Let me know how it goes.

- Paul

[Paul Shannon]

Hi Bill,

That the python test works is good news. We should be able to figure this out.

We need now to look at the sessionInfo () output from
- a working system (I believe you said that two out of three setups worked fine)
- your work laptop, the one that fails

On both, I suggest this minimal test:

> library (XMLRPC)

> xml.rpc('http://localhost:9000', 'Cytoscape.test')

> sessionInfo ()

Can you send me the output of these three commands?

Thanks!

- Paul

On Aug 30, 2012, at 1:54 PM, Bill Raynor wrote:

> Paul,
> The python approach works. I get "it works!"
> Bill
>
> On Thu, Aug 30, 2012 at 11:28 AM, Bill Raynor <brayn...@gmail.com> wrote:
> Thanks for your time Paul
>
> 1. I installed the Microsoft Loopback device
> 2. I added the RGui.exe to the firewall tables (there was nothing specific for the loopback device.)
>
> Still doesn't work. I'll install python today and try that out, too.
>
> Bill