R SIG Debian - Jan 2010 - Can I install debs over packages installed via R?

[ Kevin sent this to me but agreed that it's better to have this discussed
here. ]

On 30 January 2010 at 12:18, Kevin Donnelly wrote:
| Hi
| 
| I'm beginning to learn R,a nd I've just discovered cran2deb - what a
terrific
| resource!  Thanks for making it.
| 
| I was wondering what happens if I want to use cran2deb versions instead of the
| versions installed via R itself.  I'm on Ubuntu 9.10, and the package 
| versions go into /usr/lib/R/library, while the R versions go 
| into /usr/local/lib/R/site-library.  Is it OK just to delete them from the 
| site-library, and reinstall from cran2deb?

1)  These are different locations, so there is no conflict.

2)  R looks at the variables R_LIBS (or rather, R_LIBS_SITE and
    R_LIBS_USER). On Debian/Ubuntu, R_LIBS is set in /etc/R/Renviron to 

  # edd Apr 2003  Allow local install in /usr/local, also add a directory for
  #               Debian packaged CRAN packages, and finally the default dir 
  # edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
 
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}

3)  This means

      /usr/local/lib/R/site-library     is first and hence the default, so
      					both 'R CMD INSTALL foo_1.2-3.tar.gz'
      					and install.packages("foo") install here.
					This is where R puts things.

      /usr/lib/R/site-library		is where most r-cran-* packages go

      /usr/lib/R/library		is where base and recommended r-cran-* 
      					packages (ie those shipped with R sources)
					go

4)  You have no conflict, but if you have a library 'foo' in several
    directories, the first one found wins.

5)  On Debian, and thanks to cran2deb, I personally keep almost everything in 
    /usr/lib/R/site-library as I use cran2deb _a lot_. /usr/local is only for
    unpackage code, or things I install directly from SVN, or ...

6)  On Ubuntu, I tend to rely on install.packages() and R CMD INSTALL and the
    packages go into /usr/local/lib/R/site-library.  I do not use cran2deb on
    Ubuntu. 

Other folks may have other recommendations. Liviu seems to live happly with
cran2deb on Ubuntu. You can try it but ... buy beware.

Hope this helps, Dirk

-- 
Three out of two people have difficulties with fractions.

On Sat, Jan 30, 2010 at 5:26 PM, Dirk Eddelbuettel <edd at debian.org>
wrote:
> Other folks may have other recommendations. Liviu seems to live happly with
> cran2deb on Ubuntu. You can try it but ... buy beware.
>
Quick correction. :) I use Debian testing as my primary system, so
it's there that I install cran2deb packages. (I open Ubuntu once a
year, need-based.) I remember reading on this list, though, people
using cran2deb on Ubuntu.

Regards
Liviu

At 17:26 30/01/2010, Dirk Eddelbuettel wrote:



A lot of useful things and then
>3)  This means
>
>       /usr/local/lib/R/site-library     is first and hence the default, so
>                                         both 'R CMD INSTALL
foo_1.2-3.tar.gz'
>                                         and
install.packages("foo")
> install here.
>                                         This is where R puts things.
>
>       /usr/lib/R/site-library           is where most r-cran-* packages go
>
>       /usr/lib/R/library                is where base and 
> recommended r-cran-*
>                                         packages (ie those shipped 
> with R sources)
>                                         go
>
Could I suggest that this information be put in the readme page which 
comes up on CRAN when you click on binaries and then on debian? I did 
eventually work out two thirds of it myself but my desire to know 
where things are being put vastly outstrips my ability to work it out 
for myself.
>Hope this helps, Dirk
It certainly did.
>--
>Three out of two people have difficulties with fractions.
>
>_______________________________________________
>R-SIG-Debian mailing list
>R-SIG-Debian at r-project.org
>https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Michael Dewey
http://www.aghmed.fsnet.co.uk