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General Process: |
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[salexan5@mblog2 ~]$ cd /project/arcc<project-name>/software/conda-envs/ [salexan5@mblog2 conda-envs]$ module purge []$ module load miniconda3/24.3.0 [salexan5@mblog2 conda-envs]$ conda search r-base Loading channels: done # Name Version Build Channel ... r-base 4.3.3 hf0d99cb_1 conda-forge ... r-base 4.4.1 h1dca405_0 conda-forge [salexan5@mblog2 conda-envs]$ conda create -p r_4.3.3_env r-base=4.3.3 [salexan5@mblog2 conda-envs]$ conda activate /cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env (/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ R --version R version 4.3.3 (2024-02-29) -- "Angel Food Cake" ... |
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Note: The conda environment was created using the |
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Where are Packages Installed?
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(/cluster/medbow/project/arcc<project-name>/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" ... > Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER")) R_PLATFORM "x86_64-conda-linux-gnu" R_HOME "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R" R_LIBS_USER "/cluster/medbow/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3" R_LIBS "" R_LIBS_SITE "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/site-library" |
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(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ R R version 4.3.3 (2024-02-29) -- "Angel Food Cake" ... > .libPaths() [1] "/cluster/medbow/project/arcc<project-name>/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<project-name>/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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Remember our environment variables:
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[salexan5@mblog2 ~]$ ls /home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3 ls: cannot access '/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3': No such file or directory [salexan5@mblog2 ~]$ ls /home/salexan5<username>/R/ x86_64-pc-linux-gnu-library |
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(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 R]$ mkdir -p x86_64-conda-linux-gnu-library/4.3 (/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 R]$ R R version 4.3.3 (2024-02-29) -- "Angel Food Cake" ... > .libPaths() [1] "/cluster/medbow/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3" [2] "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library" |
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If this path IS in your You can run into dependency/version issues is if 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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# Within R:
> install.packages("stringi")
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configure: error: in `/tmp/RtmpVm7ias/R.INSTALL2ad60710733cd2/stringi':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/stringi’
The downloaded source packages are in
‘/tmp/Rtmpio5YFH/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
installation of package ‘stringi’ had non-zero exit status |
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(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda search stringi Loading channels: done No match found for: stringi. Search: *stringi* # Name Version Build Channel r-stringi 0.4_1 r3.1.3_0 pkgs/r ... r-stringi 1.8.4 r43hbd1cc82_0 conda-forge (/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda search r-stringi Loading channels: done # Name Version Build Channel r-stringi 0.4_1 r3.1.3_0 pkgs/r ... r-stringi 1.8.4 r43hbd1cc82_0 conda-forge |
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Remember: Conda r packages use the naming convention: |
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Conda Install stringi Package
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(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda install r-stringi Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env added / updated specs: - r-stringi The following NEW packages will be INSTALLED: r-stringi conda-forge/linux-64::r-stringi-1.8.4-r43hbd1cc82_0 ... Executing transaction: done |
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Where was this installed?
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The |
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[salexan5@mblog2 ~]$ ls /project/arcc<project-name>/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 stringi tcltk tools translations utils vctrs |
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conda install -c r r-essentials |
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