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.
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.
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.