[BioC] RCytoscape error with deleteSelectedEdges

[Paul Shannon]

Hi Fahim,

(I am redirecting the CC to the bioc mailing list, rather than bioc-devel, since that is the more appropriate venue for your question.)

I think you have run into version confusion -- something that gets us all sooner or later.

If you take these steps, I can pretty nearly guarantee everything will be fixed:

  1) install the latest R, 2.13.0
  2) source ("http://bioconductor.org/biocLite.R")
  3) biocLite ('RCytoscape')
  4) install the latest CytoscapeRPC.jar plugin (version 1.4) from the Cytoscape web site

Let me know how it goes -

 - Paul


On Apr 16, 2011, at 9:05 AM, Fahim Mohammad wrote:

> Hi 
> I am trying to use the following function of RCytoscape 
> 
> selectEdges (cw, c('B', 'C'))
> deleteSelectedEdges (cw)
> 
> But the function is  not recognized. So I checked the version and came to know that latest is 1.2.0 while I was using 1.0.1. The session info is shown below. 
> 
> 
> 1> sessionInfo()
> R version 2.12.1 (2010-12-16)
> 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=C              LC_MESSAGES=en_US.UTF-8   
>  [7] LC_PAPER=en_US.UTF-8       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] plyr_1.5.1       RCytoscape_1.0.1 RBGL_1.26.0      graph_1.28.0    
> [5] hash_2.1.0       RMySQL_0.7-5     DBI_0.2-5       
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.5-0  tcltk_2.12.1 tools_2.12.1 XML_3.2-0    XMLRPC_0.2-4
> 1> 
> 
> 
> I downloaded the latest .tar.gz from bioconductor site and tried to install using R CMD INSTALL RCy........1.2.0.tar.gz  but I keep on getting the following error. 
> 
> fahim at fahim-desktop:~/Downloads$ sudo R CMD INSTALL RCytoscape_1.2.0.tar.gz 
> [sudo] password for fahim: 
> * installing to library ‘/home/fahim/R/x86_64-pc-linux-gnu-library/2.12’
> * installing *source* package ‘RCytoscape’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : class "graphBase" is not exported by 'namespace:graph'       // WHAT IS THIS ?????????????????????
> ERROR: lazy loading failed for package ‘RCytoscape’
> * removing ‘/home/fahim/R/x86_64-pc-linux-gnu-library/2.12/RCytoscape’
> * restoring previous ‘/home/fahim/R/x86_64-pc-linux-gnu-library/2.12/RCytoscape’
> fahim at fahim-desktop:~/Downloads$
> 
> 
> So after unsuccessful attempt I installed again the  RCytoscape using source() and biocLite('RCy...') and the default 1.0.1  version is . But the now the functions of Rcytoscape is not working.  
> > cw <- new.CytoscapeWindow (window.title, graph=g)
> Error: could not find function "new.CytoscapeWindow"
> 
> I have no idea what is going on here.  
> 
> Any help is appreciated. 
> Thanks 
> 
> 
> 
> 
> -- 
> Fahim Mohammad 
> Bioinforformatics Lab
> University of Louisville
> Louisville, KY, USA
> Ph:  +1-502-409-1167