From Augix' Wiki

Contents 1 Regular packages 1.1 in Shell 1.2 in R 2 Packages from Bioconductor

Regular packages

in Shell

• download package (source code, eg: gem_1.0.tar.gz)

wget http://pbil.univ-lyon1.fr/gem/r_package/gem_1.0-0.tar.gz

• install gem package

R CMD INSTALL -l ~/Library/R/ gem_1.0-0.tar.gz

• configure your R_LIBS path with setenv

setenv R_LIBS ~/Library/R/

more about install R packages in shell: R: Howto install & load R library

in R

install.packages("affy",lib="~/Library/R",dependencies=TRUE)

or

install.packages("affy",lib="~/Library/R",dependencies=TRUE,contriburl="http://bioconductor.org/packages/2.1/bioc/src/contrib/")

Packages from Bioconductor

in R

source("http://bioconductor.org/biocLite.R")
biocLite("affy")