'pluginVersion' not 'version' (was Re: new Rcytoscape installation)
Paul Shannon
I renamed the method 'pluginVersion' to minimize name collisions.
I think you will find that this works:
pluginVersion (CytoscapeConnection ()) # 1.8
I have changed the documentation to match.
Thanks!
- Paul
On Apr 17, 2012, at 5:11 PM, Burak Kutlu wrote:
> Hi Paul
> Version call does not work.
> Thanks!
> -burak
>
>> cy = CytoscapeConnection ()
>> version (cy)
> Error: could not find function "version"
>>
>>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] RCytoscape_1.6.2 XMLRPC_0.2-4 graph_1.34.0
> [4] BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.2.0 RCurl_1.91-1 tools_2.15.0 XML_3.9-4
>>
>
>> RCytoscape::version (cy)
> Error: 'version' is not an exported object from 'namespace:RCytoscape'
>>
>
>
> On Apr 16, 2012, at 9:20 AM, Paul Shannon wrote:
>
>> A couple of weeks have passed since the latest release of
>>
>> R (2.15.0)
>> Bioconductor (2.10)
>> Jan Bot's CytoscapeRPC (1.8)
>> RCytoscape 1.6.2
>>
>> Even if you are conservative by nature :} please consider upgrading.
>>
>> Full instructions on how to upgrade and install can be found here:
>>
>> http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/current/index.html (look for the 'Installation' link on the top left)
>>
>>
>> Some of the new features and bug fixes:
>>
>>
>> NEW FEATURES
>>
>> o setNodeOpacityRule, controlling node fill color, border and/or label; interpolate & lookup modes both supported
>>
>> o getNodeSize
>>
>> o saveImage now supports pdf as well as png and svg formats
>>
>> o setDefaultEdgeFontSize
>>
>> o getAdjacentEdgeNames
>>
>> SIGNIFICANT USER-VISIBLE CHANGES
>>
>> o changed method names: layout -> layoutNetwork, version -> pluginVersion,
>> get/setPosition -> get/setNodePosition
>>
>> o NAMESPACE now imports four more methods from the graph package, helpful
>> for package developers using RCytoscape: edgemode, addNode, addEdge,
>> requested by Robert Flight.
>>
>> BUG FIXES
>>
>> o Changed getNodePosition node.name.