Install package on luke (or any ciment clusters)

If you want to install a package on a luke (or any ciment clusters):

Log on luke fronthead

ssh luke

note: This is always better if you do not work directly on the fronthead node but in a computation node via an interactive job. To do so you should type something like (changing teembio by the name of the project you belong to)

oarsub -I --project teembio

In the case all where all the nodes you have access to are overloaded, you can still do the package installation on the fronthead node.

When you are log on luke, you will first have to:

• define proxy settings
• load the compilation packages
• load R

export http_proxy=http://www-cache.ujf-grenoble.fr:3128
source /applis/ciment/v2/env.bash
module load gnu-devel
module load R

Then you can just open R and install the package you want as usually :

dir.create("~/MY_LUKE_R_PKGS", showWarnings = FALSE, recursive = TRUE)
install.packages("ggplot2", lib = "~/MY_LUKE_R_PKGS", repos = "http://cran.rstudio.com")

note: In this example I decided to install the ggplot2 package within a directory called MY_LUKE_R_PKGS. If you copy this directory in any ciment cluster and give refer in R the path to this one (via smth like .libPaths("~/MY_LUKE_R_PKGS") ), you will be able to use your personal packages everywhere.

note: a bench of packages already installed for luke/ciment cluster and available for everyone is available on luke at /nfs_scratch2/emabio/R_PKG_LUKE/. Feel free to use/add packages in this latter one.