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Use Case
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Consider the following use cases:
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
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The general process for this is:
Every time this is to be used:
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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_library/r_workshop/ [salexan5@mblog2 r_workshop]$ pwd /project/arcc<project-name>/software/r_library/r_workshop # Load and Start R [salexan5@mblog2 ~]$ module purge []$ module load gcc/13.2.0 r/4.4.0 [salexan5@mblog2 ~]$ R # Check current library paths: > .libPaths() [1] "/cluster/medbow/home/salexan5<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" |
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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<username>/R/x86_64-pc-linux-gnu-library/4.4" "7.3-22" "recommended" ... "XML" "XML" "/cluster/medbow/home/salexan5<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" |
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Note: We can current see packages installed:
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Update the Library Path
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Update the library paths to point to my newly created library folder, and the base packages. |
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> .libPaths(c('/project/arcc<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"
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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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# Within R:
> install.packages("Matrix")
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also installing the dependency ‘lattice’
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* DONE (Matrix)
> write.table(installed.packages()[,c(1,2,3:4)])
"Package" "LibPath" "Version" "Priority"
"lattice" "lattice" "/cluster/medbow/project/arcc<project-name>/software/r_library/r_workshop" "0.22-6" "recommended"
"Matrix" "Matrix" "/cluster/medbow/project/arcc<project-name>/software/r_library/r_workshop" "1.7-0" "recommended"
"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"
# Lets check:
[salexan5@mblog2 r_library]$ ls /project/<project-name>/software/r_library/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. |
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Update the |
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[salexan5@mblog1 r_library]$ cat r_library_test.R .libPaths(c('/project/arcc<project-name>/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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