[R] /usr/lib/R/library vs /usr/local/lib/R/site-library

[Dirk Eddelbuettel]

On Wed, Oct 29, 2003 at 07:51:16AM -0800, A.J. Rossini wrote:
> Frank E Harrell Jr <f.harrell at vanderbilt.edu> writes:
> 
> 1> I would appreciate getting a clarification of /usr/lib/R/library vs
> 1> /usr/local/lib/R/site-library.  I am running R 1.8 on Debian Linux.
> 1> On one occasion doing update.packages() resulted in versions of one
> 1> or more libraries being placed in one of these directories without
> 1> removing the old version, and the old version took precedence over
> 1> the new.  I'm sorry I did not save the steps I used.  I would
> 1> appreciate reading how best to manage libraries.  Currently I have
> 1> the following in /usr/local/lib/R/site-library: Design, Hmisc,
> 1> Rcmdr, acepack, car.  /usr/lib/R/library contains the following:
> >
> > KernSmooth  boot     eda      lqs      modreg  nnet     stepfun   ts
> > MASS        class    foreign  methods  mva     rpart    survival
> > R.css       cluster  grid     mgcv     nlme    spatial  tcltk
> > base        ctest    lattice  mle      nls     splines  tools
> >
> 
> On Debian (and I'm sure Dirk will pipe in), /usr/lib/R/library is for
> apt-installed by the core R packages, 

(i.e. r-base-core and r-recommended)

> /usr/lib/R/site-library is for
> apt-installed R packages (from CRAN, or Jim Lindsey's works), and

(or from Omegahat. [1] )

> /usr/local/lib/R/site-library where you want to put locally installed
> stuff (i.e. "install.packages()" should put there).

All correct. 

This stems from a consensus reached between Drs Bates, Eddelbuettel, Leisch
and Hornik during DSC 2003.  It is not yet fully implemented as not all 
apt-get'able Debian packages of CRAN, Omegahat, ... packages have been
rebuilt -- and thos who haven't are still installing into /usr/lib/R/library
but will install into .../site-library once rebuilt.

The broader aspects of this are outlined in a 'Debian R Policy' draft Doug
and I have been working on, on and off. A new draft is nearing completion,
and I'll make sure I'll let Frank comment too.

Dirk

[1] And one day from BioC (Tony and I are only about a good year late ;-)

-- 
Those are my principles, and if you don't like them... well, I have others.
                                                -- Groucho Marx