Creating a Shared Library of R Packages
- Simon Alexander
Goal: Demonstrate how to use an R library to create a shared set of R packages.
Use Case
Consider the following use cases:
You’re collaborating on some research and want users of the project to use the same R environment and set/version of a collection of R packages.
You’re leading a workshop and want all attendees to learn using the same environment.
In both cases we can setup an R library within a shared location, such as a project folder, which all users can access, and thus use the same set of packages.
General Process
The general process for this is:
Create a folder in a shared location.
Load and start R.
Update the library paths to point to this location.
Install R packages.
Every time this is to be used:
Load and start R.
Update the library paths to point to this location.
Example
# Create R Library folder:
[]$ cd /project/arcc/software/
[]$ mkdir -p r_library/r_workshop
[]$ cd r_library/r_workshop/
[]$ pwd
/project/<project-name>/software/r_library/r_workshop
# Load and Start R
[]$ module purge
[]$ module load gcc/13.2.0 r/4.4.0
[]$ R
# Check current library paths:
> .libPaths()
[1] "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library"Current Available R Packages
> write.table(installed.packages()[,c(1,2,3:4)])
"Package" "LibPath" "Version" "Priority"
"class" "class" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "7.3-22" "recommended"
...
"XML" "XML" "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4" "3.99-0.17" NA
"base" "base" "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library" "4.4.0" "base"
...
"utils" "utils" "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library" "4.4.0" "base"Note: We can current see packages installed:
Under our home folder.
Base packages installed as part of this R version.
Update the Library Path
> .libPaths(c('/project/<project-name>/software/r_library/r_workshop', '/apps/u/spack/gcc/12.2.0/r/4.4.0-7i7afpk/rlib/R/library'))
> write.table(installed.packages()[,c(1,2,3:4)])
"Package" "LibPath" "Version" "Priority"
"base" "base" "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library" "4.4.0" "base"
...
"utils" "utils" "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library" "4.4.0" "base"Install a package into the New Library Location
Test and Use
Error:
Success:
Warning: Remember