On 01/24/2011 10:45 AM, Kevin Wright wrote: > I currently set the Bioconductor repository in my .Rprofile using this > code (which needs editing for every version number change of > Bioconductor): > > # Choose repositories > repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", > CRANextra="http://www.stats.ox.ac.uk/pub/RWin", > BioCsoft="http://www.bioconductor.org/packages/2.7/bioc", > Rforge="http://r-forge.r-project.org")) > options(repos=repos) > rm(repos) > > I'd like to avoid editing the version number. One hack to do so is > this code that adds all repositories. > > setRepositories(ind=1:10) > r <- getOption("repos") > r <- r[!is.na(r)] > options(repos=r) > > Is there a simpler way? I've searched for quite a while without > finding an answer. > > > Incidentally, the help page for "options" says: > A Bioconductor mirror can be selected by setting > options("BioC_mirror"): the default value is > "http://www.bioconductor.org". > The word "default" is a bit confusing here, because when I start R, I see:
one possibility is to source('http://bioconductor.org/biocLite.R') in .Rprofile, after which biocinstallRepos() provides the correct bioc repositories for the version of R in use; it does clutter the .GlobalEnv a little and would be irritating if, e.g., on a laptop, internet access were slow or not reliable. For the latter I wrote makeActiveBinding("biocLite", local({ env <- new.env() function() { if (!exists("biocLite", envir=env, inherits=FALSE)) { evalq(source("http://bioconductor.org/biocLite.R", local=TRUE), env) } env[["biocLite"]] } }), .GlobalEnv) which doesn't make the connection until one accesses the biocLite variable. Martin > > R> options()$BioC_mirror > NULL > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.