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(/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ R -e 'Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER", "R_LIBS", "R_LIBS_SITE"))'
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
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> Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER"))
R_PLATFORM "x86_64-conda-linux-gnu"
R_HOME "/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env/lib/R"
R_LIBS_USER "/cluster/medbow/home/salexan5/R/x86_64-conda-linux-gnu-library/4.3"
R_LIBS ""
R_LIBS_SITE "/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env/lib/R/site-library"
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Note: The platform string value is different: |
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# Within R:
> install.packages("vctrs")
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also installing the dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’
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* DONE (vctrs) |
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Where was this installed?
| Info |
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Check |
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(/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
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> .libPaths()
[1] "/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env/lib/R/library" |
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Since I own this Conda environment, I have permission to install under: Lets check: |
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[salexan5@mblog2 ~]$ ls /project/arcc/software/conda-envs/r_4.3.3_env/lib/R/library/
base cli compiler datasets glue graphics grDevices grid lifecycle methods
parallel rlang splines stats stats4 tcltk tools translations utils vctrs |
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But What about the R_LIBS_USER Environment Variable?
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Remember our environment variables:
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[salexan5@mblog2 ~]$ ls /home/salexan5/R/x86_64-conda-linux-gnu-library/4.3 ls: cannot access '/home/salexan5/R/x86_64-conda-linux-gnu-library/4.3': No such file or directory [salexan5@mblog2 ~]$ ls /home/salexan5/R/ x86_64-pc-linux-gnu-library |
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Why is I own this Conda environment, so have permission to install under: Since this folder is missing, it is not being picked up and used by the |
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If you manually create this folder then |
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(/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env/lib/R - lets check: |
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) [salexan5@mblog2 ~R]$ ls /mkdir -p x86_64-conda-linux-gnu-library/4.3 (/cluster/medbow/project/arcc/software/conda-envs/r_4.3.3_env/lib/R/library/ base cli compiler datasets glue graphics grDevices grid lifecycle methods parallel rlang splines stats stats4 tcltk tools translations utils vctrs |
| Info |
The ~) [salexan5@mblog2 R]$ R R version 4.3.3 (2024-02-29) -- "Angel Food Cake" ... > .libPaths() [1] "/cluster/medbow/home/salexan5/R/x86_64-conda-linux-gnu-library/4.3" [2] "/cluster/medbow/project/arcc/software/conda-envs/r_4.3location is where R will additionally look for outside packages not directly part of this Conda environment .3_env/lib/R/library" |
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Using the |
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Try Installing stringi Package
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The Conda install of the R package is installed within the same location as the R install.packages() function.
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Warning: Conda related R_LIBS_USER - Check!
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Question: Should you manually create the |
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First, we would suggest that unless you are confident in self-managing your Conda/R environments then do not. If this is not in your |
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If this path IS in your You can run into dependency/version issues is you want to use version X of a package in one Conda environment, but version Y in another. You can only have one version in this folder. |
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We have observed that some times this folder have been automatically created. Best thing is to always check and set the |
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Anaconda: R Essentials
Although we do not recommend installing Anaconda (unless you are comfortable with how it works and modifies your home environment), it does provide an R Essentials bundle which “includes approximately 80 of the most popular scientific packages for the R programming language.“
...