Installing R packages

Part of the reason R has become so popular is the vast array of packages available at the cran and bioconductor repositories. In the last few years, the number of packages has grown exponentially!

This is a short post giving steps on how to actually install R packages. Let’s suppose you want to install the ggplot2 package. Well nothing could be easier. We just fire up an R shell and type:

> install.packages("ggplot2")

In theory the package should just install, however:

• if you are using Linux and don’t have root access, this command may not work. If you use Ubuntu then this isn’t a problem.
• if you have limited space in /home/ then you may want to install the package in the non-default directory.
• you will be asked to select your local mirror, i.e. which server should you use to download the package.
• if you have a proxy, then you may run into problems.

Installing packages in a different directory

First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory /data/Rpackages/ After creating a package directory, to install a package we use the command:

> install.packages("ggplot2", lib="/data/Rpackages/")
> library(ggplot2, lib.loc="/data/Rpackages/")


It’s a bit of a pain having to type /data/Rpackages/ all the time. To avoid this burden,  we create a file .Renviron in our home area, and add the line R_LIBS=/data/Rpackages/ to it. This means that whenever you start R, the directory /data/Rpackages/ is added to the list of places to look for R packages and so:

> install.packages("ggplot2")
> library(ggplot2)

just works!

Setting the repository

Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:

• create a file .Rprofile in your home area.
• Add the following piece of code to it:


cat(".Rprofile: Setting UK repository\n")
r = getOption("repos") # hard code the UK repo for CRAN
r["CRAN"] = "http://cran.uk.r-project.org"
options(repos = r)
rm(r)

Or as Hadley pointed out, this could be condensed to:

cat(".Rprofile: Setting UK repository\n")
options(repos = c(CRAN = "http://cran.uk.r-project.org/"))

but you would deleted any other repositories you have set – say the r-forge repository (thanks to Kevin for pointing this out).

Obviously, you don’t need the cat statement, but I find it helpful to remind me that I’ve set this default. Especially if you have a laptop and you a lot of travelling.

I found this tip in a stackoverflow answer .

Setting your http proxy

This section is an update and follows a comment from Sean Carmody below.

If you have a http proxy, then one method of setting the proxy in R is to use the sys.system command, viz.

Sys.setenv(http_proxy="http://myproxy.example.com:8080")


Sys.setenv(http_proxy=”http://myproxy.example.com:8080″)