[Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)

[Dan Tenenbaum]

----- Original Message -----
> From: "Martin Morgan" <mtmorgan at fhcrc.org>
> To: bioc-devel at 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
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> 
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