Building R on enigma [2005-06-20]
---------------------------------

NOTE: Before building R, the ATLAS linear algebra libraries should be
installed in /usr/local/lib so that they will be picked up by the
`configure' script.  If the ATLAS libraries are not there, then a
reference BLAS implementation will be used instead and there will be a
significant performance decrease.

ATLAS libraries built for Enigma/Usher can be found in
/home/bst/student/rpeng/install/atlas.


The current R source tarball (version 2.1.1) is located at

http://cran.r-project.org/src/base/R-2/R-2.1.1.tar.gz

The current R sources will always be available at
http://cran.r-project.org/.  We will also maintain an older version of
R concurrent with the most recent released version.  The older version
will always be one minor release number less than the current version
(and the most recent patch release for that version).  Therefore, if
2.1.1 is the current version, the older version is 2.0.1.  The sources
for version 2.0.1 are available at

http://cran.r-project.org/src/base/R-2/R-2.0.1.tgz


After downloading/untar-ing, run the `configure' script.  The argument
passed to the `--prefix' switch may need to be changed depending on
where we actually want to install R and on the version number.

./configure --with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh --with-tcltk --prefix=/usr/local/R-2.1.1
make
make install


Then start R and run (as root):

## Install all CRAN packages
allpkgs <- CRAN.packages()[, 1]
install.packages(allpkgs)

## Install all Bioconductor packages
source("http://www.bioconductor.org/getBioC.R")
getBioC("all")

## Install Bioconductor metadata packages (this is big)
library(reposTools)
reps <- getOptReposList()
for(i in c(6,10,11)) {
    install.packages2(repEntry = getRepEntry(reps, i))
}