I've been using EBSeq for a few things lately, and have had trouble getting some of the dependencies installed -- in particular, gplots doesn't seem to be readily available for R 2.14, 2.15, etc. Judging by my Google searches, others have been having the same problems; see e.g.

http://stackoverflow.com/questions/16091096/can-not-install-ggplot-package-in-r-2-14-1

The general error message is of the form:

Warning in install.packages :
   package 'gplots' is not available (for R version 2.14.1)

Since I'm not an R expert, it took me a long time to find a solution; here's what I cooked up:

curl -O http://cran.ma.imperial.ac.uk/src/contrib/Archive/gplots/gplots_2.6.0.tar.gz
tar xzf gplots_2.6.0.tar.gz

cat <<EOF > /tmp/inst.sh

options(repos=structure(c(CRAN="http://cran.ma.imperial.ac.uk")))

install.packages("gtools")
install.packages("gdata")
install.packages("gplots", repos = NULL, type="source")
EOF

Rscript /tmp/inst.sh

Hope this saves someone some time! Comments and updates welcome -- I'm sure this isn't the best way to do it.

--titus

p.s. I hate R.

p.p.s. Although to be fair this kind of problem crops up everywhere in any useful programming language, because SOFTWARE SUCKS.