Hello, I have just tried to install bioconductor. I noted some problems (at least for me) when using getBioC() to install packages. Here is my setup: R 1.7.0 under redhat 7.1 linux. I currently put my R libraries in ~/langs/R/library since I do not have access to the /usr/lib/R/library. So I have export R_LIBS=$HOME/langs/R/library in my .bashrc Then, within R I did: > source("http://www.bioconductor.org/getBioC.R") [fine] > getBioC(libName="all") Running getBioC version 1.2.29.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Please select an installation directory: 1:~/langs/R/library 2:/usr/lib/R/library Selection: 1 [1] "Installing reposTools ..." ERROR: cannot write to or create directory '/usr/lib/R/library' Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : Failed to install package Biobase So, despite me asking it to install in my home dir, it tried to update /usr/lib/R/library. I checked my paths: > .libPaths() [1] "~/langs/R/library" "/usr/lib/R/library" so that presumably is fine. I think I found the problem: the installPack() function does not currently accept the "destdir" argument. When I amended this function, it seemed to work okay. [One other problem I noted; during the install process, it asked me several times if I wanted to install standard packages like "eda", "methods", "tcltk", "stepfun". Is this intended?] Here is a possible patch against the current getBioC.R. Stephen *** /tmp/getBioC.R~ Sat May 17 16:48:02 2003 --- /tmp/getBioC.R Sat May 17 16:48:02 2003 *************** *** 236,242 **** ## Download and install download.file(sourceUrl, fileName, mode = getMode(platform), quiet = TRUE, method=method) ! installPack(platform, fileName) if (!(i %in% installed.packages()[,"Package"])) stop(paste("Failed to install package",i)) unlink(fileName) --- 236,242 ---- ## Download and install download.file(sourceUrl, fileName, mode = getMode(platform), quiet = TRUE, method=method) ! installPack(platform, fileName, destdir) if (!(i %in% installed.packages()[,"Package"])) stop(paste("Failed to install package",i)) unlink(fileName) *************** *** 288,297 **** } ## Installs a given package ! installPack <- function(platform, fileName){ if(platform == "unix"){ cmd <- paste(file.path(R.home(), "bin", "R"), ! "CMD INSTALL", fileName) system(cmd) }else{ if(platform == "windows"){ --- 288,297 ---- } ## Installs a given package ! installPack <- function(platform, fileName, destdir){ if(platform == "unix"){ cmd <- paste(file.path(R.home(), "bin", "R"), ! "CMD INSTALL -l", destdir, fileName) system(cmd) }else{ if(platform == "windows"){