Seth et al, After installing R-2.3.0 (release) plus BioC using getBioC() (default packages), which reported using BioC 1.8 and installed what would seem to be the correct version of reposTools (1.10.0), using reposTools results in setting the "repositories2" option to paths that include BIOCRel1.7 rather than BIOCRel1.8. I'm happy to flood you with system details if needed, but it seems not to be architechure/OS dependent - I see the behavior both on solaris10 and on a windows (XP) system. This seems to derive from 1.7 being specifies in the zzz.R file of the distribution. > getOption("repositories2") NULL > library(reposTools) > getOption("repositories2") CRAN BIOCRel1.7 "http://www.bioconductor.org/CRANrepository" "http://www.bioconductor.org/packages/bioc/1.7" BIOCData BIOCExdata "http://www.bioconductor.org/packages/data/annotation/1.7" "http://www.bioconductor.org/packages/data/experiment/1.7" BIOCCourses BIOCcdf "http://www.bioconductor.org/repository/Courses" "http://www.bioconductor.org/packages/data/annotation/1.7" BIOCprobes BIOCOmegahat "http://www.bioconductor.org/packages/data/annotation/1.7" "http://www.bioconductor.org/packages/omegahat/1.7" BIOCLinds "http://www.bioconductor.org/packages/lindsey/1.7" -Steve ***************************************************************** Steve Roels, Ph.D. Senior Scientist I Computational Biology Millennium Pharmaceuticals, Inc. ***************************************************************** This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. Thank you.

Hi Steve, Thanks for the report. The real bug here is that getBioC() pulled in reposTools at all. We are now relying entirely on CRAN-style package repositories. The reposTools stuff is deprecated --- we are not hosting repositories that will work for it (except for old BioC versions). So to install packages, we recommend: source("http://bioconductor.org/biocLite.R") OR source("http://bioconductor.org/getBioC.R") And then getBioC("somePackageHere") OR biocLite("somePackageHere") Either one should pullin dependencies, etc. If you want to see a list of the repositories that we host for the BioC packages try: library("Biobase") biocReposList() Best, + seth