----- Original Message ----- > From: "Martin Morgan" <mtmor...@fhcrc.org> > To: bioc-devel@r-project.org > Sent: Wednesday, May 7, 2014 10:07:10 PM > Subject: Re: [Bioc-devel] Tracking Current release > (http://www.bioconductor.org/packages/current redirect to > http://www.bioconductor.org/packages/2.14) > > Hi Don -- > > On 05/07/2014 06:21 PM, Don Armstrong wrote: > > I maintain a collection of Debian packages of CRAN and BioC[1] for > > public use; currently, whenever BioC makes a new release, it > > requires > > manual intervention for me to point at the new release location. > > > > It would be helpful if there was a > > http://www.bioconductor.org/packages/current redirect to the > > current > > release, or if there was another easily parsable method to obtain > > the > > current bioC release version. > > Bioconductor releases are tied to R versions and the 'current' Bioc > for a > particular R, in a brand new installation, is > > source("http://bioconductor.org/biocLite.R") > biocVersion() > > (this is BiocInstaller::biocVersion(), where the biocLite.R script > has arranged, > modulo MITM concerns below, to install the version of the > BiocInstaller package > relevant to your version of R). I personally think of this as the > canonical > location, but... > > http://bioconductor.org/packages/release goes to the current release > 'biocViews', with packages under release/ being the current release > versions. > http://bioconductor.org/bioc-version is probably what you'll end up > using > (though I believe it's hand curated), and
This is automatically generated, as is http://bioconductor.org/js/versions.js which also includes the devel version number. Dan > tools:::.BioC_version_associated_with_R_version (this is a function > in R-3.1) > gives the version that R thinks is the current BioC version (this can > become > stale, e.g., R-3.0.1 was released when BioC-2.12 was the current > version, but > part way through the R point release BioC 2.13 became available [or > at least, > that's how I remember it]). > > > FWICT, neither http://bioconductor.org/getBioC.R nor > > http://bioconductor.org/biocLite.R encode that information > > either,[2] > > unless that's what CURRENT_R_DEVEL_VERSION <- "2.14.0" is supposed > > to > > be. > > > > > > 1: http://debian-r.debian.net/ > > > > 2: I should also point out that the current methodology of > > installing > > BioC using code from a remote host is problematic as it exposes > > users to > > MITM attacks because it is never checked for authenticity via PGP > > or at > > the very least, SSL. As such, sourcing that script and using > > variables > > populated by it isn't really acceptable. > > Of course this is a valid concern and we can work toward a more > secure approach. > > Perhaps I could take the opportunity to ask a naive question about > debian binary > distributions of R. What is the directory into which packages are > installed by > sudo? In particular, are they unversioned, /usr/lib/R/library etc, as > opposed to > say /usr/lib/R-3.1/library ? I'm asking because a number of users > seem to show > up with say R-3.1 reporting a mix of R-3.1 and R-3.0.2 packages, > usually to ill > effect; this is not necessarily likely for user-installed packages, > because the > system directories won't be writeable and R will prompt with a > versioned > directory ~/R/x86_64-unknown-linux-gnu-library/3.1 as the location to > install > libraries. I'm wondering if mixed package versions would happen if > their package > manager failed to remove previously installed packages from the > /usr/lib/R/library directory, or if the user installed multiple > versions of R. > Of course this could merely reflect users installing R without the > help of > package managers, and either way it might point to changes in the way > R installs > itself. > > Martin > > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel