[BioC] problem getting setNodeColorRule from RCytoscape to work

[Tony]

Paul Shannon <pshannon at ...> writes:

> 
> Hi Tony,
> 
> Thanks for sending the session and version info.
> 
> Please see comments inline below...
> 
> 
> There are updates for a few of your packages, and for Cytoscape itself.  One 
plausible cause is RCurl.  Your
> version 1.6-7, and the current release is 1.91-1.  
> 
> May I suggest the following?  Upgrade RCurl (see 
http://www.omegahat.org/RCurl/) and then, if you don't
> mind, restart R, and send me the exact transcript of your R session, the few 
lines of code needed to
> reproduce the error.  When I see them in context (if the RCurl update does not 
fix the problem) then I could do
> a better job of figuring things out.  Meanwhile: I am sorry that you are 
running into trouble.
> 
> Also, I should warn you!  We have a new release of R, of Bioconductor, and 
RCytoscape.  Though it can be a little
> painful to make the transition, we generally encourage everyone to stay 
current.  Since the release
> happened only yesterday, finding the fix for your problem should be something 
we can do separately form
> the upgrade we might soon recommend.
> 
>  - Paul
> 

Hi Paul,

Problem solved! I followed your suggestions to upgrade all the packages, R, 
RCurl, RCytoscape, Rcytoscaperpc, still not working, then I also upgraded 
Cytoscape itself to 2.8.2, them everything work charmingly!

Indeed, stay current! Thank you for your help and your wonderful software! Also 
attach my new sessionInfo in case someone need to check against.

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RCytoscape_1.6.1 XMLRPC_0.2-4     graph_1.34.0    

loaded via a namespace (and not attached):
[1] BiocGenerics_0.2.0 RCurl_1.91-1       tools_2.15.0       XML_3.9-4         
>