Installing custom R packages
Installation of R packages for all cluster users can be requested via the helpdesk,
which will add them to a future RPlus module.
Making a new RPlus module is not something the helpdesk can do quickly though:
we maintain a list of more than 1500 R packages and compiling a new module can take a lot of time.
It is also possible to install customR packages in a tmp group folder yourself
and optionally share it with your colleagues as long as they have access to the same group folder.
Create location for custom R packages and prepend that to the search path for R packages
First you will need to choose a location where you want to install your custom R packages.
This path needs to be added to the ${R_LIBS} environment variable in your ${HOME}/.Renviron config file.
1. Create a ${HOME}/.Renviron file
touch ${HOME}/.Renviron
This will create a .Renviron file in your home dir if you did not already have one.
If the file already exists the touch command will only update the last modification time stamp of the file and leave the content unchanged.
2. Add ${R_LIBS} to your ${HOME}/.Renviron file
If the path you chose for your custom R package is in the tmp01 folder of the group named my-favorite-group
and the R version for which you want to compile your extra R packages is 4.2.2,
then add something like this to your ~/.Renviron file:
R_LIBS="/groups/my-favorite-group/tmp01/R-packages/x86_64-pc-linux-gnu-library/4.2:${R_LIBS}"
Note ${R_LIBS} versus ${R_LIBS_USER}
The R documentation instructs users to set ${R_LIBS_USER} instead of ${R_LIBS}.
${R_LIBS_USER} is used together with ${R_LIBS_SITE} and hard-coded paths added at compile time to create ${R_LIBS}.
When you use ${R_LIBS_USER} though, your custom folder for R packages will end up in the wrong order in ${R_LIBS}
when you mix custom R packages with R packages from other sources like for example the RPlus module.
Note % expansions do not work in ${R_LIBS}
The %p and %v expansions for platform and version, which are available for ${R_LIBS_USER}
cannot be used with ${R_LIBS}, so something like this
R_LIBS="/groups/my-favorite-group/tmp01/R-packages/%p-library/%v:${R_LIBS}"
will not work.
Note about version numbers in the path
When you upgrade to another patch level for the same major & minor version of R (e.g. 4.2.2 -> 4.2.3),
then you can use the same path.
But you will want to update the path in your ${HOME}/.Renviron and recompile the R packages
when upgrading to another minor or another major version (e.g. 4.2.2 -> 4.3.1 or 4.2.2 -> 5.0.1).
3. Make sure the custom path added to ${R_LIBS} exists
Create the folder if it does not already exist. E.g.:
mkdir -p -m 770 "/groups/my-favorite-group/tmp01/R-packages/x86_64-pc-linux-gnu-library/4.2"
Next, load either a bare R or load RPlus, which is a bundle of lots of R packages already pre-installed on Gearshift.
module load RPlus
R
Now, use the .libPaths() function in R to check the value(s) for the paths where R will search for extra packages.
By default new R packages will be installed in the first folder reported by .libPaths()
R> .libPaths()
[1] "/groups/my-favorite-group/tmp01/R-packages/x86_64-pc-linux-gnu-library/4.2"
[2] "/apps/software/R/4.2.2-foss-2022a-bare/lib64/R/library"
If the .libPaths() function does not list your folder for custom R packages (first),
but for example only the library folder for the loaded R version itself like this
R> .libPaths()
[1] "/apps/software/R/4.2.2-foss-2022a-bare/lib64/R/library"
Then this most likely means that the path specified in ${R_LIBS_USER} does not exist yet;
In that case quit R, double check for typos and whether the folder was created correctly on the file system.
Install custom R packages
With your custom folder for R packages present on the file system and listed as the first item by the .libPaths function,
you can now install packages. Below are examples of installing packages from different sources.
A. Install R package from the Comprehensive R Archive Network (CRAN) repository
Load and start R.
module load RPlus
R
Use the install.packages() function
to install packages from CRAN.
E.g. to install a package named packageName:
R> install.packages('packageName')
B. Install R package from the BioConductor repository
Load and start R.
module load RPlus
R
BioConductor has its own R package to manage package installations.
It is named BiocManager and can be installed from CRAN.
Install BiocManager in R if it is not already installed:
R> if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
Next, use BiocManager to install BioConductor packages. E.g.:
R> BiocManager::install(c('myFavoritePackage', 'packageAlsoNeeded'))
C. Install R package from an archive file without (CRAN) repository
If the (version of the) R package you need is not available from CRAN nor from BioConductor nor from another R repository,
but you do have the source code of the package in a compressed archive file, then you can try to install that using the R CMD INSTALL command.
Note that this is sub optimal; when the code you need is available from a curated repo like CRAN or BioConductor, use those repos instead.
In this example, we use abctools version 1.1.4 (and it was downloaded from CRAN, but it could have been fetched from another repo/source).
Since we know the URL, the command wget can be used to download the *.tar.gz archive.
You can also use for example rsync to copy the compressed archive to Gearshift
if you have the file on your local machine.
wget https://cran.r-project.org/src/contrib/abctools_1.1.4.tar.gz
Next, we need to load R (but do not start R yet)
module load RPlus
Run the command below to install the package from the compressed archive file.
R CMD INSTALL path/to/your/uploaded/abctools_1.1.4.tar.gz
D. Install R package from a GitHub repository
Load and start R.
module load RPlus
R
You can use the remotes::install_github command from the remotes package to install other packages from a GitHub repository.
If not already present the remotes package must be installed from CRAN first.
In the example below we will install the package methylCIPHER from a GitHub repo.
When no version is specified, the remotes::install_github command will install the latest commit from whatever the main branch is.
WARNING: this may be unstable, unreleased, untested code. In order to install the latest released version use ref = github_release().
You can also specify a specific version number; see the documentation for remotes::install_github
R> install.packages('remotes')
R> library('remotes')
R> remotes::install_github('MorganLevineLab/methylCIPHER', ref = github_release())