7  Installing software in R

A short tutorial that shows how to find and install packages in R.

7.1 Where do we find installed packages in R?

A typical installation of RStudio involves also the installation of R, which includes some default packages. These packages can be loaded into the current environment using the function library(). For example:

# load the mtcars package
library("mtcars")

In some cases, there are some packages that might have been installed in non-standard locations with the purpose of better version control and space usage. But, how do we get access to those packages? If interested in using a specific package in R that has been installed in a non-standard location, you can use the .libPaths() function to load the path of the directory containing the installation of a specific package. For example:

# Tell R where the DESeq2 package is installed in /data/apps/R/4.3.2
.libPaths("/data/apps/R/4.3.2/DESeq2")
# Load the DESeq2 package using library()
library(DESeq2)
# DESeq2 functions ready to use

7.2 But what is .libPaths()?

.libpaths() is a function for setting the library search path (directory), which is where R looks for installed packages. R will have a default location in your system for installing packages where .libpaths() will look for them. In the following example, /home/user/R/x86_64-pc-linux-gnu-library/4.3 is the default directory where R will look for packages:

# if you run .libpaths() with no arguments it gives you the current directory where R will look for installed packages:
.libPaths()
[1] "/home/jcarpinteyro/R/x86_64-pc-linux-gnu-library/4.3" "/opt/R/4.3.2/lib/R/library"

7.3 What if I want to install a new package in R?

If the package of interest has not been installed yet, you can install it by yourself using the functions in How to install software/packages in R?

By default, all the packages each user install by themselves will be installed in the R default directory. For example:

# New packages will be installed in "/home/user/R/x86_64-pc-linux-gnu-library/4.3" when using install.packages()
.libPaths()
[1] "/home/user/R/x86_64-pc-linux-gnu-library/4.3" "/opt/R/4.3.2/lib/R/library"
# Install the dplyr package using install.packages()
install.packages("dplyr")

You may have heard about install.packages() so let’s take a peek behind the curtain on what it does!

Using the command line (UNIX or Linux) you could go to /home/user/R/x86_64-pc-linux-gnu-library/4.3 and you will see a new directory that contains all the necessary files to run the functions of the dplyr package:

user@sandbox:~$ cd R/x86_64-pc-linux-gnu-library/4.3/
user@sandbox:~/R/x86_64-pc-linux-gnu-library/4.3$ ls
abind    BiocGenerics  bitops        dplyr          futile.options    GenomicRanges  locfit          Rcpp           S4Arrays   SparseArray           zlibbioc
BH       BiocParallel  DelayedArray  formatR        GenomeInfoDb      IRanges        MatrixGenerics  RcppArmadillo  S4Vectors  SummarizedExperiment
Biobase  BiocVersion   DESeq2        futile.logger  GenomeInfoDbData  lambda.r       matrixStats     RCurl          snow       XVector

7.4 How to install packages in R?

In R we have several ways to install software packages and the most common way is to do so is using the function install.packages() . This function will try to download and locally install packages available at CRAN (The Comprehensive R Archive Network), which is a general purpose repository of packages. A usage example of the install.packages() could look as:

# Install tidyverse from CRAN
install.packages("tidyverse")
# Load tidyverse
library("tidyverse")

Depending on the scientific field you might require to install and use more specialized packages. For example, Bioconductor is an open-development software project for the analysis of genomic data. Bioconductor can be considered a repository of packages and, in order to install packages from this repository, we could use the function BiocManager::install(). A typical use of this function can look as:

# Use the install function from BiocManager to install DESeq2
BiocManager::install("DESeq2")
library("DESeq2")