It is easier than that. Use http://www.bioconductor.org/packages/release/bioc
or http://www.bioconductor.org/packages/devel/bioc /Henrik On Mon, Jan 24, 2011 at 10:56 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > 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. > ______________________________________________ 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.