We encourage users to maintain their own R packages. This ensures that the user has no discontinuity in their workflow waiting for packages to be installed and that packages work with the user’s chosen, loaded R module. R packages are built specifically to a version of R and may not work properly if a different version of R is loaded. O2’s LMOD “module” feature allows users to quickly and easily switch between R versions.
||shows the versions of R installed on O2|
||loads an individual module|
||unloads an individual module|
||shows the current version of R loaded|
||from R, shows currently-installed packages|
Setting up a personal R library
This sets up an environment to store R packages locally. From R, all packages will be installed and saved to this R library by default. It is recommended to use a separate R library for each version of R selected (swap
Version Selected for the R chosen, like 3.2.5 or 3.3.3, etc). Multiple members of a group can share an R library saved in a group-accessible location by following the
In O2 bash ($):
mfk8@login02:~$ mkdir -p ~/R-VersionSelected/library mfk8@login02:~$ echo 'R_LIBS_USER="~/R-VersionSelected/library"' > $HOME/.Renviron mfk8@login02:~$ export R_LIBS_USER="/home/user123/R-VersionSelected/library"
Starting R Interactively
R should not be executed from the login servers (login0X). Instead, launch an interactive session, specifying the memory requirements. R does not implicitly use multiple cores unless the code is parallelized, so 1 core is sufficient. Here’s a model R workflow:
mfk8@login02:~$ srun --pty -p interactive -t 0-12:00 --mem 8000 -n 1 /bin/bash mfk8@compute-a-01-01:~$ module load gcc/6.2.0 R/3.2.5 #or version chosen mfk8@compute-a-01-01:~$ R > #notice how the prompt changes.
Installing Packages Using Bioconductor
The majority of bio-related packages can be downloaded through Bioconductor.
Bioconductor packages are listed at http://www.bioconductor.org/packages/release/BiocViews.html#___Software
Installing Packages Using CRAN
install.packages() searches CRAN by default and asks you to select a mirror, but a repos can be specified using this command:
A list of CRAN available packages is available at http://cran.r-project.org/web/packages/
Installing Packages from github using devtools
devtools package, users can install software from github repositories. First install and call library on devtools, then use the
> install.packages('devtools') > library(devtools) > install_github('username/repo')
Installing Packages from Local File
If there is a package that needs to be manually downloaded (via wget/curl/etc), user should put the package in
~/R-VersionSelected/library and install it like this:
In R (>):
Conversely, if all dependencies are already existing for the package, R CMD INSTALL can be used from the command line (on an interactive compute node):
mfk8@login02:~$ srun --pty -p interactive -t 0-12:00 --mem 8000 /bin/bash mfk8@compute-a-01-01:~$ module load gcc/6.2.0 R/3.2.5 #or version selected mfk8@compute-a-01-01:~$ R CMD INSTALL downloadedRPackage.tar.gz
At the top of any script that uses an R package, the package must be explicitly called via
User case for a new R session, with these packages already installed: