For what it's worth, I use the scriipt below (via ~/bin/update.r) which is
also an example script in the littler package.
It _explicitly_ restricts the update to
/usr/local/lib/R/site-library
so that the update from R is kept separate from the update via the Debian or
Ubuntu package manager.
Hope this helps, Dirk
#!/usr/bin/r -t
#
# a simple example to update packages in /usr/local/lib/R/site-library
# parameters are easily adjustable
## adjust as necessary, see help('download.packages')
repos <- "http://cran.r-project.org";
## or use BioC's repo list if Biobase is installed:
suppressMessages(rc <- require(Biobase))
if (rc) {
repos <- Biobase:::biocReposList()
}
## this makes sense on Debian where no package touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"
## simply unrolling of all unlink over all files 'repos*' in $TMP
clearCache <- function() {
sapply(list.files(path=tempdir(), pattern="libloc*", full.names=TRUE), unlink)
}
## Always clear caches of remote and local packages
clearCache()
## r use requires non-interactive use
update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)
## Always clear caches of remote and local packages
clearCache()
--
Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com
_______________________________________________
R-SIG-Debian mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
