{"type":"doc","content":[{"type":"paragraph","content":[{"text":"Goal","type":"text","marks":[{"type":"strong"}]},{"text":": Understand R environments build with Conda.","type":"text"}]},{"type":"panel","attrs":{"panelType":"error"},"content":[{"type":"paragraph","content":[{"text":"Note","type":"text","marks":[{"type":"strong"}]},{"text":": There is a known vulnerability with R versions less than 4.4.0.","type":"text"}]},{"type":"paragraph","content":[{"text":"This page uses R version 4.3.3. This page is purely for example since as of the date of creating this page there were issues using an r-base/4.4.1.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"error"},"content":[{"type":"paragraph","content":[{"text":"I am hoping in a few weeks/months the 4.4.x base will be stable and I’ll update the examples.","type":"text"}]}]},{"type":"rule"},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"1"},"outline":{"value":"false"},"style":{"value":"none"},"type":{"value":"list"},"printable":{"value":"true"}},"macroMetadata":{"macroId":{"value":"3d98b5ca-ba17-4a1e-aee2-cc74027c79d9"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"03e74fc4-f4be-4893-9260-4217662897a0"}},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Basic R Conda Environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"General Process:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ cd /project//software/conda-envs/\n[]$ module purge\n[]$ module load miniconda3/24.3.0\n[]$ conda search r-base\nLoading channels: done\n# Name Version Build Channel\n...\nr-base 4.3.3 hf0d99cb_1 conda-forge\n...\nr-base 4.4.1 h1dca405_0 conda-forge\n[]$ conda create -p r_4.3.3_env r-base=4.3.3\n[]$ conda activate /cluster/medbow/project//software/conda-envs/r_4.3.3_env\n(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ R --version\nR version 4.3.3 (2024-02-29) -- \"Angel Food Cake\"\n...","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Note: The conda environment was created using the ","type":"text"},{"text":"-p","type":"text","marks":[{"type":"code"}]},{"text":" option, so it was installed under the current working directory, which in the case was: ","type":"text"},{"text":"/project/arcc/software/conda-envs","type":"text","marks":[{"type":"code"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Where are Packages Installed?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Lets look at the environment variables:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ R -e 'Sys.getenv(c(\"R_PLATFORM\", \"R_HOME\", \"R_LIBS_USER\", \"R_LIBS\", \"R_LIBS_SITE\"))'\nR version 4.3.3 (2024-02-29) -- \"Angel Food Cake\"\n...\n> Sys.getenv(c(\"R_PLATFORM\", \"R_HOME\", \"R_LIBS_USER\"))\n R_PLATFORM \"x86_64-conda-linux-gnu\"\n R_HOME \"/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R\"\n R_LIBS_USER \"/cluster/medbow/home//R/x86_64-conda-linux-gnu-library/4.3\"\n R_LIBS \"\"\n R_LIBS_SITE \"/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R/site-library\"\n","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Note","type":"text","marks":[{"type":"strong"}]},{"text":": The platform string value is different: ","type":"text"},{"text":"x86_64-conda-linux-gnu","type":"text","marks":[{"type":"code"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Try Installing ","type":"text"},{"text":"vctrs","type":"text","marks":[{"type":"code"}]},{"text":" Package","type":"text"}]},{"type":"codeBlock","content":[{"text":"# Within R:\n> install.packages(\"vctrs\")\n...\nalso installing the dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’\n...\n* DONE (vctrs)","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Where was this installed?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Check ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":":","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ R\nR version 4.3.3 (2024-02-29) -- \"Angel Food Cake\"\n...\n> .libPaths()\n[1] \"/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R/library\"","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Since I ","type":"text"},{"text":"own","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" this Conda environment, I ","type":"text"},{"text":"have permission","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" to install under: ","type":"text"},{"text":"/project/arcc/software/conda-envs/r_4.3.3_env/lib/R","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"paragraph","content":[{"text":"Lets check:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ ls /project//software/conda-envs/r_4.3.3_env/lib/R/library/\nbase cli compiler datasets glue graphics grDevices grid lifecycle methods \nparallel rlang splines stats stats4 tcltk tools translations utils vctrs","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"But What about the ","type":"text"},{"text":"R_LIBS_USER","type":"text","marks":[{"type":"code"}]},{"text":" Environment Variable?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Remember our environment variables:","type":"text"}]},{"type":"codeBlock","content":[{"text":"R_LIBS_USER \"/cluster/medbow/home//R/x86_64-conda-linux-gnu-library/4.3\"\nR_HOME \"/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R\"","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ ls /home//R/x86_64-conda-linux-gnu-library/4.3\nls: cannot access '/home//R/x86_64-conda-linux-gnu-library/4.3': No such file or directory\n[]$ ls /home//R/\nx86_64-pc-linux-gnu-library","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Since this folder is missing, it is not being picked up and used by the ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":" command.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Can I Create this Folder?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"If you ","type":"text"},{"text":"manually","type":"text","marks":[{"type":"em"}]},{"text":" create this folder then ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":" does pick it up.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ mkdir -p x86_64-conda-linux-gnu-library/4.3\n(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ R\nR version 4.3.3 (2024-02-29) -- \"Angel Food Cake\"\n...\n> .libPaths()\n[1] \"/cluster/medbow/home//R/x86_64-conda-linux-gnu-library/4.3\"\n[2] \"/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R/library\"","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Using the ","type":"text"},{"text":"install.packages()","type":"text","marks":[{"type":"code"}]},{"text":" command within R will ","type":"text"},{"text":"now","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" look/install packages into this folder that could be ","type":"text"},{"text":"shared","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" across multiple Conda environments using this version of R.","type":"text"}]}]},{"type":"mediaSingle","attrs":{"layout":"center","width":365,"widthType":"pixel"},"content":[{"type":"media","attrs":{"width":365,"alt":"image-20240729-234708.png","id":"8279e1d5-261f-42f9-8d77-b88cdb358902","collection":"contentId-2189492237","type":"file","height":167}},{"type":"caption","content":[{"text":"Example of sharing R Packages across multiple Conda Environments.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Should I Create this Folder?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Question","type":"text","marks":[{"type":"strong"}]},{"text":": Should you manually create the ","type":"text"},{"text":"~/R/x86_64-conda-linux-gnu-library/X.Y/","type":"text","marks":[{"type":"code"}]},{"text":" folder?","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"First, we would suggest that unless you are confident in ","type":"text"},{"text":"self-managing","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" your Conda/R environments then do not. ","type":"text"}]},{"type":"paragraph","content":[{"text":"If this is not in your ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":", then it will force all R package installs to be contained under the Conda environment.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"If this path ","type":"text"},{"text":"IS","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" in your ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":", across multiple conda environments, then all the environments will install into and look/share this folder.","type":"text"}]},{"type":"paragraph","content":[{"text":"You can run into ","type":"text"},{"text":"dependency/version issues","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" if you want to use version X of a package in one Conda environment, but version Y in another. ","type":"text"},{"text":"You can only have one version in this folder","type":"text","marks":[{"type":"em"}]},{"text":".","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"We have observed that some times this folder have been ","type":"text"},{"text":"automatically","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" created.","type":"text"}]},{"type":"paragraph","content":[{"text":"Best thing is to ","type":"text"},{"text":"always","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" check and set the ","type":"text"},{"text":".libPaths()","type":"text","marks":[{"type":"code"}]},{"text":" to you necessary needs.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Try Installing ","type":"text"},{"text":"stringi","type":"text","marks":[{"type":"code"}]},{"text":" Package","type":"text"}]},{"type":"codeBlock","content":[{"text":"# Within R:\n> install.packages(\"stringi\")\n...\nconfigure: error: in `/tmp/RtmpVm7ias/R.INSTALL2ad60710733cd2/stringi':\nconfigure: error: C++ compiler cannot create executables\nSee `config.log' for more details\nERROR: configuration failed for package ‘stringi’\n* removing ‘/cluster/medbow/project//software/conda-envs/r_4.3.3_env/lib/R/library/stringi’\n\nThe downloaded source packages are in\n ‘/tmp/Rtmpio5YFH/downloaded_packages’\nUpdating HTML index of packages in '.Library'\nMaking 'packages.html' ... done\nWarning message:\nIn install.packages(\"stringi\") :\n installation of package ‘stringi’ had non-zero exit status","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Conda environments are not the same as the System/compute nodes - libraries and behavior can be different.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Conda Install ","type":"text"},{"text":"stringi","type":"text","marks":[{"type":"code"}]},{"text":" Package: Search","type":"text"}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ conda search stringi\nLoading channels: done\nNo match found for: stringi. Search: *stringi*\n# Name Version Build Channel\nr-stringi 0.4_1 r3.1.3_0 pkgs/r\n...\nr-stringi 1.8.4 r43hbd1cc82_0 conda-forge\n\n(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ conda search r-stringi\nLoading channels: done\n# Name Version Build Channel\nr-stringi 0.4_1 r3.1.3_0 pkgs/r\n...\nr-stringi 1.8.4 r43hbd1cc82_0 conda-forge","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Remember","type":"text","marks":[{"type":"strong"}]},{"text":": Conda r packages use the naming convention: ","type":"text"},{"text":"r-","type":"text","marks":[{"type":"code"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Conda Install ","type":"text"},{"text":"stringi","type":"text","marks":[{"type":"code"}]},{"text":" Package","type":"text"}]},{"type":"codeBlock","content":[{"text":"(/cluster/medbow/project//software/conda-envs/r_4.3.3_env) []$ conda install r-stringi\nChannels:\n - conda-forge\n - defaults\nPlatform: linux-64\nCollecting package metadata (repodata.json): done\nSolving environment: done\n\n## Package Plan ##\n environment location: /cluster/medbow/project//software/conda-envs/r_4.3.3_env\n added / updated specs:\n - r-stringi\n\nThe following NEW packages will be INSTALLED:\n r-stringi conda-forge/linux-64::r-stringi-1.8.4-r43hbd1cc82_0\n...\nExecuting transaction: done","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Where was this installed?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"conda install","type":"text","marks":[{"type":"code"}]},{"text":" command (whatever the type of package/library) installs within the conda environment .","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[salexan5@mblog2 ~]$ ls /project//software/conda-envs/r_4.3.3_env/lib/R/library/\nbase cli compiler datasets glue graphics grDevices grid lifecycle methods parallel \nrlang splines stats stats4 stringi tcltk tools translations utils vctrs","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Anaconda: R Essentials","type":"text"}]},{"type":"paragraph","content":[{"text":"Although we do not recommend installing ","type":"text"},{"text":"Anaconda","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.anaconda.com/"}}]},{"text":" (unless you are comfortable with how it works and modifies your home environment), it does provide an ","type":"text"},{"text":"R Essentials bundle","type":"text","marks":[{"type":"link","attrs":{"href":"https://docs.anaconda.com/working-with-conda/reference/r-language-pkg-docs/#r-essentials-bundle"}}]},{"text":" which “","type":"text"},{"text":"includes approximately 80 of the most popular scientific packages for the R programming language.","type":"text","marks":[{"type":"em"}]},{"text":"“","type":"text"}]},{"type":"codeBlock","content":[{"text":"conda install -c r r-essentials","type":"text"}]},{"type":"rule"},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"0fa9cbf1-57a6-4d35-ad95-10850999d415"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[333.0]},"content":[{"type":"paragraph","content":[{"text":"Prev","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Where are R Packages Installed on the Cluster?","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2189066318"}}]},{"text":" ","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[326.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Workshop Home","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Using R and RStudio on the Cluster","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2136014965"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[349.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"Next","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"R Packages and System Modules","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2189230106"}}]}]}]}]}]},{"type":"paragraph","content":[{"text":" ","type":"text"}]},{"type":"paragraph","content":[{"text":" ","type":"text"}]}],"version":1}

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