Tamas,
Great question.
On 4 November 2006 at 11:55, Tamas K Papp wrote:
| I have searched the archive for the solution of this question, but
| couldn't find anything, so I thought I would ask here.
It has been discussed not that long ago on r-sig-debian, feel free to
subscribe there as you may find the list useful for all matters Debian and R.
| I am using R on a Debian (testing) system. Many of the R packages I
| use are installed as .deb packages, those which are not available in
| this format I install using install.packages.
|
| When calling update.packages, sometimes the R repository version is
| more recent than the Debian package, and update.packages offers to
| update it which I don't want because the new debianized version will
| be out soon. Is it possible to have update.packages recognize that
| these are "systemwide" packages and ignore them when updating? Or is
| manual selection of what to update the only option?
Let's recall that we have three locations for R packages under Debian (and
hence also Ubuntu et al):
i) /usr/lib/R/library
used *exclusively* by r-base-core (and e.g. not even by
r-recommended such as r-cran-vr, r-cran-boot, ...)
ii) /usr/lib/R/site-library
used *exclusively* by Debian (or Ubuntu) supplied packages
that you can updated with apt-get et al (provided the
maintainer stays current)
iii) /usr/local/lib/R/site-library
used for the rest
The key is that these are non-overlapping which you can employ with
update.packages() provided you tell update.packages() to limit itself to
the directory in iii). Which is as simple as saying
> update.packages(lib.loc="/usr/local/lib/R/site-library")
Now, for added bonus, the script 'update.r' in the littler package (version
0.0.8 or later) does all that for you. So after an initial
$ sudo apt-get install littler
all you need is
$ sudo /usr/share/doc/littler/examples/update.r
Cheers, Dirk
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
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