Hi, I just tried using getBioC() but got the following error message. Is getBioC() supposed to get developmental packages instead of stable packages, or has it not been updated for the stable releases of R 2.3.0 and Bioconductor 1.8? biocLite() is working fine, but I liked the longer default list of getBioC. Thanks, Jenny > source("http://www.bioconductor.org/getBioC.R") > ls() [1] "getBioC" > getBioC() Running getBioC version 0.8 with R version 2.3.0 Error in getBioC() : Please check back soon, currently the BioConductor developmental packages are not available for R 2.3 users. > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Hi Jenny, I've been working a little bit on fixing and cleaning the biocLite() and getBioC() functions. Both should be ready to work with R 2.3 (and then hit Bioconductor 1.8) or R 2.4 (and then hit Bioconductor devel). The only difference between these 2 functions is the list of packages that you get when you use them with no arguments. With this: > source('http://bioconductor.org/biocLite.R') > biocLite() you get this (with R 2.3 and 2.4): [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2" "limma" "marray" "matchprobes" [16] "multtest" "reposTools" "ROC" "vsn" "xtable" But with this: > source('http://bioconductor.org/getBioC.R') > getBioC() you get the same as above plus: "edd" "globaltest" "makecdfenv" "pamr" "siggenes" "sma" "statmod" "tkWidgets" "widgetTools" Both functions install the "Depends" and "Imports" dependencies too but you can override this behaviour by giving your own 'dependencies' argument. Please, let me know of any problem. Thanks, H. -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319