R SIG Debian - May 2010 - running a locally built R-devel with libraries from Debian installation

Hi,

What is the best way to tell a locally-built R-devel (somewhere in the
user home directory) to use the libraries from the Debian installation
(i.e. /usr/local/lib/R/site-library and /usr/lib/R/site-library).  I
suppose this would take setting one or all of R_LIBS, R_LIBS_SITE,
R_LIBS_USER in ~/.Renviron, but that would also affect the Debian R in
the system so is not an option.  How do R Debianers handle this
situation?

Cheers,

-- 
Seb

On 9 May 2010 at 16:33, Sebastian P. Luque wrote:
| Hi Dirk,
| 
| On Sun, 9 May 2010 16:04:52 -0500,
| Dirk Eddelbuettel <edd at debian.org> wrote:
| 
| [...]
| 
| > /etc/R/ -- and see help(Startup) for the files.  All also explained in
| > the R Inst. and Admin manual.
| 
| > If you don't have the softlinks from /etc/R/ then it is
| 
| >    $whereEver/R/etc/
| 
| > instead.
| 
| Thanks, I'm familiar with these, but I was referring to the local
| R-devel so was hoping for something that didn't involve modifying these
| files because they'd get wiped out every time R-devel is rebuilt.
| Perhaps there's just no way around that.

There are still a number of possibilities in the R Inst + Admin manual; a
simple one would be to set the env. var R_LIBS via /etc/environment.  

But you need to tell us what you can or cannot do or want to do.  The 'No
Psychics here' rule applies for you too :)

-- 
  Regards, Dirk

On 9 May 2010 at 18:50, Sebastian P. Luque wrote:
| On Sun, 9 May 2010 17:57:40 -0500,
| Dirk Eddelbuettel <edd at debian.org> wrote:
| 
| > The Debian package should only set these env vars if these are
| > otherwise unset:
| 
| > edd at ron:~> Rscript -e 'print(.libPaths())' ## default [1]
| > "/usr/local/lib/R/site-library"
"/usr/lib/R/site-library" [3]
| > "/usr/lib/R/library" edd at ron:~>
R_LIBS_SITE="/tmp" Rscript -e
| > 'print(.libPaths())' [1] "/tmp"
"/usr/lib/R/library" edd at ron:~>
| > R_LIBS_USER="/tmp" Rscript -e 'print(.libPaths())' [1]
"/tmp"
| > "/usr/local/lib/R/site-library" [3]
"/usr/lib/R/site-library"
| > "/usr/lib/R/library" edd at ron:~>
| 
| > There may well be a bug lurking somewhere but at leats here I got to
| > modify libPaths on the fly.
| 
| > Good enough?
| 
| Great, I guess that's what I'm trying to get at: one would have to
start
| R-devel with a long string.  I thought there would be a way to just do
| 'R' or '~/src/R-devel/bin/R' and then have a mechanism in the
user
| startup files to ensure that Debian site libraries are added only when
| using R-devel.  Thanks Dirk, that should get me en route!

Another possibility is to use ~/.Rprofile and to directly set this as an
argument to to the .libPaths() function -- see help(.libPaths).

-- 
  Regards, Dirk