The directories in R where the packages are stored are called the libraries. The terms package and library are sometimes used synonymously and there has been discussion amongst the community to resolve this.
https://www.r-bloggers.com/2013/01/packages-v-libraries-in-r/
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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.
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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.
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Example
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# Create R Library folder: [salexan5@mblog2 ~]$ cd /project/arcc/software/ [salexan5@mblog2 software]$ mkdir -p r_library/r_workshop [salexan5@mblog2 r_library]$ cd r_workshop/ [salexan5@mblog2 r_workshop]$ pwd /project/arcc/software/r_library/r_workshop # Load and Start R [salexan5@mblog2 ~]$ module load gcc/13.2.0 r/4.4.0 |
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[salexan5@mblog2 ~]$ R # |
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Check current library paths:
> .libPaths()
[1] "/cluster/medbow/home/salexan5/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" |
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Create Current Available R Packages
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> write.table(installed.packages()[,c(1,2,3:4)])
"Package" "LibPath" "Version" "Priority"
"class" "class" "/cluster/medbow/home/salexan5/R/x86_64-pc-linux-gnu-library/4.4" "7.3-22" "recommended"
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"XML" "XML" "/cluster/medbow/home/salexan5/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"
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"utils" "utils" "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/library" "4.4.0" "base" |
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Note: We can current see packages installed:
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Update the Library Path
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> .libPaths(c('/project/ |
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arcc/software/r |
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_library/r_workshop', '/apps/u/spack/gcc/12.2.0/r/4.4.0-7i7afpk/rlib/R/library')) |
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> 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" |
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Note: We can currently only see the base packages since we haven’t yet installed anything into |
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Install a package into the New Library Location
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# Within R: > install.packages("Matrix") |
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... also installing the dependency ‘lattice’ ... * DONE (Matrix) > write.table(installed.packages()[,c(1,2,3:4)]) "Package" "LibPath" "Version" "Priority" "lattice" "lattice" "/cluster/medbow/project/arcc/software/r_library/r_workshop" "0.22-6" "recommended" "Matrix" "Matrix" "/cluster/medbow/project/arcc/software/r_library/r_workshop" "1.7-0" "recommended" "base" "base" "/apps/u/spack/gcc/ |
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13.2.0/r/4.4.0- |
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pvzi4gp/rlib/R/library" "4.4.0" |
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"base" ... "utils" "utils" "/apps/u/spack/gcc/ |
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13.2.0/r/4.4.0- |
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pvzi4gp/rlib/R/library |
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" "4.4.0" "base"
# Lets check:
[salexan5@mblog2 r_library]$ ls r_workshop/
lattice Matrix |
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Test and Use
Error:
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[salexan5@mblog1 r_library]$ cat r_library_test_fail.R
library(Matrix)
[salexan5@mblog1 r_library]$ Rscript r_library_test_fail.R
Error in library(Matrix) : there is no package called ‘Matrix’
Execution halted
# The Matrix package is NOT available under our default library location. |
Success:
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Update the |
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[salexan5@mblog1 r_library]$ cat r_library_test.R
.libPaths(c('/project/arcc/software/r_library/r_workshop', '/apps/u/spack/gcc/12.2.0/r/4.4.0-7i7afpk/rlib/R/library'))
library(Matrix)
[salexan5@mblog1 r_library]$ Rscript r_library_test.R
[salexan5@mblog1 r_library]$ |
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Warning: Remember
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Within this example, by default this is a SHARED project location. Anyone who has access to this project and thus this shared library can update it. If an individual performs an |
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The project users will need to collaborate and come up with some form of data plan and/or process for the management of this shared library. |
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