[Bioc-devel] R v3.0.0: It's now official and BioC devel needs some updates

On Sun, Dec 16, 2012 at 1:16 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:

From http://stat.ethz.ch/R-manual/R-devel/NEWS:

  "It is intended that this version will be released as R 3.0.0."


They've already changed the R-devel version number from 2.16.0 to
3.0.0, which causes biocLite() et al. to fail, e.g.

source("http://www.bioconductor.org/biocLite.R")

Installing package into 'C:/Users/hb/R/win-library/3.0'
(as 'lib' is unspecified)
Warning: unable to access index for repository http://www.bioconductor.org/packa
ges/2.12/bioc/bin/windows/contrib/3.0

   package 'BiocInstaller' is available as a source package but not as a binary

'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="http://www.bioconductor.org/packages/2.12/bioc")'
Warning message:
package 'BiocInstaller' is not available (for R Under development)

This now works.

Note that we have not yet updated our devel build machines to R-3.0.0,
so there may be binary incompatibilities in Windows and Mac packages.
If in doubt, install from source.

Dan

/Henrik