<\/p>\n
You can find this information by running <\/p>\n To get a list of installed packages, execute <\/p>\n If you would like to get additional information about the installed packages you can access it using If priority is <\/p>\n Method 1: Install from CRAN directly<\/b>. A package can be installed using Note:<\/b> Regardless of the method you used to install the package, it has to be loaded into the workspace before you can actually use it. To load it, type <\/p>\n A package can be removed using <\/p>\n To check for updates run <\/p>\n To install a newer version of a package run <\/p>\n <\/p>\n You can view the default path R is using to install new packages running <\/p>\n You can list and run non-default versions of R available on the cluster, running the following commands at the Linux prompt:<\/p>\n Below is a simple process for installing the updated versions of all of your packages into a new version of R.<\/p>\n 1. Run the old version of R you have been using:<\/p>\n 2. Run the following code in the old version of R:<\/p>\n 3. Run the new version of R:<\/p>\n 4. Run the following code in the new version of R:<\/p>\n What version of R do I run? You can find this information by running R.version.string at the R prompt: # get version of R > R.version.string [1] R version 4.1.2 (2021-11-01) What R packages do I already have? To get a list of installed packages, execute library() at the R prompt. R will first list…<\/p>\n","protected":false},"author":1692,"featured_media":0,"parent":51114,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/pages\/129507"}],"collection":[{"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/users\/1692"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/comments?post=129507"}],"version-history":[{"count":9,"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/pages\/129507\/revisions"}],"predecessor-version":[{"id":140766,"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/pages\/129507\/revisions\/140766"}],"up":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/pages\/51114"}],"wp:attachment":[{"href":"https:\/\/www.bu.edu\/tech\/wp-json\/wp\/v2\/media?parent=129507"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}R.version.string<\/code> at the R prompt:<\/p>\n# get version of R<\/span>\r\n> <\/span>R.version.string<\/span>\r\n[1] R version 4.1.2 (2021-11-01)<\/span><\/code><\/pre>\nWhat R packages do I already have?<\/h2>\n
library()<\/code> at the R prompt. R will first list all the packages installed in your local R directory and then it will list all of the packages installed globally on your system:<\/p>\n# list all R packages installed<\/span>\r\n> <\/span>library()<\/span>\r\n\r\nPackages in library '\/usr1\/scv\/ktrn\/R\/x86_64-pc-linux-gnu-library\/4.1':\r\n\r\ncombinat\t\tcombinatorics utilities\r\nproftools\t\tOutput Processing Tools for R\r\nrgl 3D visualization device system (OpenGL)\r\n\r\nPackages in library '\/share\/pkg.7\/r\/4.1.2\/install\/lib64\/R\/library':\r\n\r\nKernSmooth Functions for kernel smoothing for Wand & Jones (1995)\r\nMASS Support Functions and Datasets for Venables and Ripley's MASS <\/span><\/code><\/pre>\nHow can I find additional information about R packages I have?<\/h2>\n
installed.packages()<\/code> at the R prompt. A more concise output can be obtained running installed.packages()[ ,c(1,3,4)]<\/code>. This will include the name of the package, its version and \u201cpriority\u201d information:<\/p>\n# Obtain information about installed R packages<\/span>\r\n> <\/span>installed.packages()[ ,c(1,3,4)]<\/span>\r\n\r\n Package Version Priority\r\nrtweet \"rtweet\" \"0.7.0\" NA\r\nMASS \"MASS\" \"7.3-51.6\" \"recommended\"\r\nMatrix \"Matrix\" \"1.2-18\" \"recommended\"\r\nbase \"base\" \"4.1.2\" \"base\"\r\n... <\/span><\/code><\/pre>\n\u201cbase\u201d<\/code>, the package is already loaded into your workspace, so all its functions are available upon opening R.
\nIf priority is \u201crecommended\u201d<\/code>, then the package was installed with base R.
\nIf priority is \u201cNA\u201d<\/code>, then the package is an optional package. Both “recommended” and “NA” packages have to be loaded using library()<\/code> command before using them.<\/p>\nHow do I install a new package?<\/h2>\n
install.packages(\"package name<\/span>\")<\/code> at the R prompt. You can also provide a pathname to install R package at a specific location: install.packages(\"package name<\/span>\", lib=\"\/my\/own\/R-packages\/<\/span>\")<\/code>. If the argument lib<\/code>\u00a0is omitted it defaults to the first directory in .libPaths()<\/code>.<\/p>\n# Install dplyr package<\/span>\r\n> <\/span>install.packages(\"dplyr\")<\/span>\r\n\r\n<\/span><\/code>Method 2: Install from source<\/b>. At the Linux prompt download the R package my_package.tar.gz<\/span> and use R CMD INSTALL<\/code> command:<\/pre>\n# Download rgl package<\/span>\r\nscc1% <\/span>wget http:\/\/cran.r-project.org\/src\/contrib\/dplyr_1.0.7.tar.gz<\/a><\/span>\r\n\r\n# Install rgl package<\/span>\r\nscc1% <\/span>R CMD INSTALL dplyr_1.0.7.tar.gz<\/span>\r\n<\/code><\/pre>\nlibrary(my_package<\/span>)<\/code> at the R prompt.<\/p>\nHow can I remove a package?<\/h2>\n
remove.packages(\"package name<\/span>\")<\/code> at the R prompt:<\/p>\n# Remove rgl package<\/span>\r\n> <\/span>remove.packages(\"dplyr\")<\/span>\r\n<\/code><\/pre>\nHow can I check if there are updates for the installed packages?<\/h2>\n
old.packages()<\/code> at the R prompt. You will be asked to specify the CRAN mirror. Then R will list all the projects that have a newer version.<\/p>\n# Check for updates<\/span>\r\n> <\/span>old.packages() <\/span>\r\n\r\n--- Please select a CRAN mirror for use in this session ---\r\nLoading Tcl\/Tk interface ... done \r\n... <\/span><\/code><\/pre>\nHow can I update a package?<\/h2>\n
update.packages()<\/code> at the R prompt. R will list all the packages that have newer versions and will offer to download and install the updates.<\/p>\n# Update all outdated packages<\/span>\r\n> <\/span>update.packages() <\/span>\r\n\r\n...\r\n\r\n# Update dplyr package only<\/span>\r\n> <\/span>update.packages( oldPkgs=\"dplyr\" ) <\/span> \r\n\r\n--- Please select a CRAN mirror for use in this session ---\r\nLoading Tcl\/Tk interface ... done \r\n... \r\n<\/span><\/code><\/pre>\nWhat is the default path R uses to install new packages?<\/h2>\n
.libPaths()<\/code> at the R prompt:<\/p>\n# Get the default R paths<\/span>\r\n> <\/span>.libPaths()<\/span>\r\n\r\n[1] \"\/usr1\/scv\/ktrn\/R\/x86_64-pc-linux-gnu-library\/4.0\"\r\n[2] \"\/share\/pkg.7\/r\/4.1.2\/install\/lib64\/R\/library\"<\/span><\/code><\/pre>\nHow can I run another R version installed on the SCC?<\/h2>\n
# List all R versions installed on the SCC<\/span>\r\nscc1% <\/span>module spider R<\/span>\r\n<\/code><\/pre>\nHow do I upgrade the packages I have installed so that they are accessible by the new version of R? <\/a><\/h2>\n
scc1% <\/span>module load R\/4.0.2<\/span>\r\nscc1% <\/span>R<\/span><\/code><\/pre>\n> <\/span>packages <- installed.packages()[,\"Package\"]<\/span>\r\n> <\/span>save(packages, file=\"Rpackages.Rds\")<\/span><\/code><\/pre>\nscc1% <\/span>module load R\/4.1.2<\/span>\r\nscc1% <\/span>R<\/span><\/code><\/pre>\n> <\/span>load(\"Rpackages\")<\/span>\r\n> <\/span>install.packages(packages)<\/span><\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"