Skip to content

Installing R packages on Bianca

R on UPPMAX course

What is a package, really?

  • An R package is essentially a contained folder and file structure containing R code (and possibly C/C++ or other code) and other files relevant for the package e.g. documentation(vignettes), licensing and configuration files.

  • Let us look at a very simple example 

   $ git clone git@github.com:MatPiq/R_example.git

   $ cd R_example

   $ tree
   .
   ├── DESCRIPTION
   ├── NAMESPACE
   ├── R
   │   └── hello.R
   ├── man
   │   └── hello.Rd
   └── r_example.Rproj

Installing your own packages

Sometimes you will need R packages that are not already installed. The solution to this is to install your own packages. - These packages will usually come from CRAN (https://cran.r-project.org/) - the Comprehensive R Archive Network, or - sometimes from other places, like GitHub or R-Forge

Here we will look at installing R packages with automatic download and with manual download. It is also possible to install from inside Rstudio.

Methods

  • setup (first time)
  • automatic download and install from CRAN
  • automatic download and install from GitHub
  • manual download and install

setup (first time)

https://uppmax.github.io/bianca_workshop/rpackages/#setup

  • We need to create a place for the own-installed packages to be and to tell R where to find them. The initial setup only needs to be done once, but separate package directories need to be created for each R version used.

  • R reads the $HOME/.Renviron file to setup its environment. It should be created by R on first run, or you can create it with the command: touch $HOME/.Renviron

NOTE: In this example we are going to assume you have chosen to place the R packages in a directory under your home directory. As mentioned, you will need separate ones for each R version.

If you have not yet installed any packages to R yourself, the environment file should be empty and you can update it like this: 

    echo R_LIBS_USER=\"$HOME/R-packages-%V\" > ~/.Renviron

If it is not empty, you can edit $HOME/.Renviron with your favorite editor so that R_LIBS_USER contain the path to your chosen directory for own-installed R packages. It should look something like this when you are done:

    R_LIBS_USER="/home/u/user/R-packages-%V"

| NOTE: Replace /home/u/user with the value of $HOME. Run echo $HOME to see its value. | NOTE: The %V should be written as-is, it's substituted at runtime with the active R version.

For each version of R you are using, create a directory matching the pattern used in .Renviron to store your packages in. This example is shown for R version 4.0.4:

    mkdir -p $HOME/R-packages-4.0.4

Automatical download and install from CRAN

https://uppmax.github.io/bianca_workshop/rpackages/#automatical-download-and-install-from-cran

Note

You find a list of packages in CRAN (https://cran.r-project.org/) and a list of repos here: https://cran.r-project.org/mirrors.html

  • Please choose a location close to you when picking a repo. 
R --quiet --no-save --no-restore -e "install.packages('<r-package>', repos='<repo>')"

install.packages('<r-package>', repos='<repo>')

In either case, the dependencies of the package will be downloaded and installed as well.

Automatic download and install from GitHub

https://uppmax.github.io/bianca_workshop/rpackages/#automatic-download-and-install-from-github

If you want to install a package that is not on CRAN, but which do have a GitHub page, then there is an automatic way of installing, but you need to handle prerequsites yourself by installing those first. - It can also be that the package is not in as finished a state as those on CRAN, so be careful.

Note

To install packages from GitHub directly, from inside R, you first need to install the devtools package. Note that you only need to install this once.

This is how you install a package from GitHub, inside R:

    install.packages("devtools")   # ONLY ONCE
    devtools::install_github("DeveloperName/package")

Manual download and install

https://uppmax.github.io/bianca_workshop/rpackages/#manual-download-and-install

If the package is not on CRAN or you want the development version, or you for other reason want to install a package you downloaded, then this is how to install from the command line: 

    R CMD INSTALL -l <path-to-R-package>/R-package.tar.gz

NOTE that if you install a package this way, you need to handle any dependencies yourself.

Note

Places to look for R packages

  • CRAN (https://cran.r-project.org/)
  • R-Forge (https://r-forge.r-project.org/)
  • Project's own GitHub page
  • etc.

Example — Install Tidycmprsk

tidycmprsk on GitHub

Info

The tidycmprsk package provides an intuitive interface for working with the competing risk endpoints. The package wraps the cmprsk package, and exports functions for univariate cumulative incidence estimates with cuminc() and competing risk regression with crr().

Install on Rackham

You can install this for yourself by beginning on rackham. Do

module load R_packages/4.1.1
and then, within R, do

install.packages('tidycmprsk')

You will see two questions to answer yes to:

Warning in install.packages("tidycmprsk") :
      'lib = "/sw/apps/R_packages/4.1.1/rackham"' is not writable
    Would you like to use a personal library instead? (yes/No/cancel) yes

and

Would you like to create a personal library
    '~/R/x86_64-pc-linux-gnu-library/4.1'
    to install packages into? (yes/No/cancel) yes

This will then to an extended installation process that also does some updates. This creates a directory ~/R that contains the installations and updates of R packages.

Transfer to the Wharf

After installation, the next step is to copy the contents of this directory over to bianca so that it is the same directory within your bianca home directory.

Make sure you are in your home directory. Then connect to the bianca wharf. Replace the name and project with your bianca user name and project.

sftp douglas-sens2017625@bianca-sftp

You log in here like you log into bianca: the first password is your password followed by the 6-digit authenticator code, the second password (if required for you) is only your password.

Once sftp has connected, the contents of the current directory can be listed with

dir

It should look like this:

sftp> dir
douglas-sens2017625

Now cd to this directory, which is your wharf directory within your project.

sftp> cd douglas-sens2017625/
sftp> dir
sftp>

If you have not uploaded anything to your wharf, this will be empty. It might have a few things in it.

Now, upload your (whole) R directory here.

sftp> put -r R

This will take a while to upload all the files. When it has completed, quit.

sftp> quit
  • Now, log into bianca using the shell, or using the web interface and start a terminal.
  • Once you have a bianca shell, change to your wharf directory within your project. Replace my user and project with yours.
cd /proj/sens2017625/nobackup/wharf/douglas/douglas-sens2017625

Within this directory should be your R directory.

[douglas@sens2017625-bianca douglas-sens2017625]$ ls -l
total 1892
drwxrwxr-x  3 douglas douglas    4096 Mar  2 14:27 R

Sync from Wharf to Home directory

  • Now sync this to your home directory:
[douglas@sens2017625-bianca douglas-sens2017625]$ rsync -Pa R ~/

Start an R session and load the new package

To use R_packages/4.1.1 with these new installations/updates, change to the directory you want to work in, load the R_packages/4.1.1 module. Substitute your directory for my example directory.

[douglas@sens2017625-bianca douglas-sens2017625]$ cd /proj/sens2017625/nobackup/douglas/
    [douglas@sens2017625-bianca douglas]$ module load R_packages/4.1.1

Then start R, and load the new package.

[douglas@sens2017625-bianca douglas]$ R

    R version 4.1.1 (2021-08-10) -- "Kick Things"
    Copyright (C) 2021 The R Foundation for Statistical Computing
    ....
    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    > library(tidycmprsk)
    >