I am using the latest Bioconductor developement version on Windows. The command library(affy) works fine from the R GUI. But I am not able to import any packages (e.g. affy) when I use the ESS+XEmacs or simply Rterm shell mode. I get the following error: I think that it may be due to some extra work the package upload routine tries to do like adding "Vignettes" menu to the GUI and fails to do so in the Rterm mode. What is the workaround? Thanks in advance, mushtaq ----------error start----------------------- > library(affy) ************* affy: development version ************* ************* IMPORTANT: you need the latest versions of the required packages too. ************* Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Creating a new generic function for "summary" in package reposTools Synching your local package management information ... Attaching package `reposTools': The following object(s) are masked from package:base : summary Error in paste(menus[1:(length(menus) - counter)], sep = "", collapse = "/") : only 0's may mix with negative subscripts Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Error in paste(menus[1:(length(menus) - counter)], sep = "", collapse = "/") : only 0's may mix with negative subscripts Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses) : Class "AffyBatch" extends an undefined class ("exprSet" Error in library(affy) : .First.lib failed > --------error end---------------- [[alternate HTML version deleted]]

> I am using the latest Bioconductor developement version on Windows. > The command library(affy) works fine from the R GUI. > But I am not able to import any packages (e.g. affy) when I use the > ESS+XEmacs or simply Rterm shell mode. I get the following error: > I think that it may be due to some extra work the package upload > routine tries to do like adding "Vignettes" menu to the GUI and fails to > do so in the Rterm mode. It appears that the package widgetTools (which is called by affy) tries to check if it is under GUI mode or not before adding a Vignette tab to the GUI menubar. However, the current check that it is using is if(interactive), which is still TRUE even in Rterm. We're looking at finding a mechanism to detect if it is inded Rgui instead of Rterm ... -J