Hi I have been trying to load the affy package not very sucessfully (details of what I did bellow) I am using a G4 Mac running the OSX Panther and I have the R version: 1.9.0. I don't know if the affy package simply won't run on the panther OSX - I have been sucessful in installing UNIX packages in the Mac R, but those didn't have any C code or things more complex and I randomly know that at least one function of the affy package (rma) has some C code. any help would be greatly appreciated! Thank you very much for helping running this wonderful system and for making all these fantastic tools available. what I did: packages menu and then under bioconductor I tried to download the affy bundle that results in: local({source(paste(getOption('BIOC'), 'getBioC.R',sep='/'), local=TRUE); getBioC('affy', destdir=.libPaths()[1])}) it doesn't work I get an error saying that it wasn't found in any respository (I copied the message bellow) I also tried to download the package to my computer and tried to install it, but unfortunately it doesn't install either: finally, when I installed BioConductor I had gotten some error messages as well: I reproduce some of them error installing the Affy package from the Menu Package => BioConductor => AffyBundle: [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.4/package/Source" [1] "Download complete." [1] "Installing affy" Note: Package affy not found in any known repository. Note: Package affydata not found in any known repository. [1] "Attempting to download affyPLM from http://www.bioconductor.org/repository/release1.4/package/Source" [1] "Download complete." [1] "Installing affyPLM" [1] "Attempting to download matchprobes from http://www.bioconductor.org/repository/release1.4/package/Source" [1] "Download complete." [1] "Installing matchprobes" Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users error when trying to install the affy package from the local disk: > install.from.file() npackage installation failed (one of the errors I got when trying to install BioConductor): previously I installed BioConductor and I also got may of those warnings (I copy here one of them) [1] "Installing XML" Note: Package XML not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [[alternative HTML version deleted]]

Hi Tiago, You could also ask this question on the R-SIG-MAC mailing list: https://stat.ethz.ch/mailman/listinfo/r-sig-mac r-sig-mac@stat.math.ethz.ch Eventually, Bioconductor may provide MacOS X binaries of its R packages, but for now, you need to install source packages on MacOS X (some of which contain C code), so you definitely need the Apple Developer Tools installed. It would help to have an I.T. administrator who knows a bit about Unix/Linux. When you download the R 1.9.1 for MacOS X installer from CRAN, there should be an option to install the XML libraries required by the XML package for R. The readers of the R-SIG-MAC list would know more than me about XML/Mac installation. Regards, James