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