I have just upgraded to 2.0.1 (patched) and am in the process of updating my Bioconductor installation (BTW, OS is RedHat 9). I had some problems using getBioC(), which I now believe were due to being incredibly unlucky in my timing (was the main repository off-line or in flux in some way today?). Thus, I tried to use install.packages2() on some individual packages. When I try to install GO, a secondary R process eventually takes up all my available RAM (a paltry 400M on this machine) and the machine just thrashes. When I kill that R process, I get the errors below and my command prompt back. Any ideas? Lots of other packages seem to require GO, so this is a real roadblock for me. Thanks in advance, Jenny ################ my session ################# R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 Patched (2004-11-22), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. WARNING: UTF-8 locales are not currently supported > options(STERM='iESS', editor='emacsclient') > library(reposTools) Loading required package: tools > install.packages2("GO", develOK=TRUE) Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download GO from http://www.bioconductor.org/data /metaData-devel/" [1] "Download complete." [1] "Installing GO" * Installing *source* package 'GO' ... ** R ** data ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'GO' Formats: text html latex example GO text html latex GOALLLOCUSID text html latex example GOBPANCESTOR text html latex example GOBPCHILDREN text html latex example GOBPOFFSPRING text html latex example GOBPPARENTS text html latex example GOCCANCESTOR text html latex example GOCCCHILDREN text html latex example GOCCOFFSPRING text html latex example GOCCPARENTS text html latex example GOLOCUSID text html latex example GOLOCUSID2ALLGO text html latex example GOLOCUSID2GO text html latex example GOMFANCESTOR text html latex example GOMFCHILDREN text html latex example GOMFOFFSPRING text html latex example GOMFPARENTS text html latex example GOQC text html latex GOTERM text html latex example /usr/local/lib/R/bin/INSTALL: line 1: 19406 Done echo "invisible(.libPaths(c(\"${lib}\", .libPaths()))); tools:::.install_package_indices(\".\", \"${R_PACKAGE_DIR}\")" 19407 Terminated | R_DEFAULT_PACKAGES=NULL LANG=C "${R_EXE}" --vanilla >/dev/null ERROR: installing package indices failed ** Removing '/usr/local/lib/R/library/GO' ** Restoring previous '/usr/local/lib/R/library/GO' >From URL: http://www.bioconductor.org/data/metaData-devel/ GO version 1.6.6 Warning message: Installation of package GO had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > q() Save workspace image? [y/n/c]: n Process R finished at Tue Nov 23 16:25:03 2004