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<code>Rscript</code> will automatically pass scripting-appropriate options < | <code>Rscript</code> will automatically pass scripting-appropriate options <code>--slave</code> and <code>--no-restore</code> to the R interpreter. These also imply the <code>--no-save</code> option, preventing the creation of useless workspace files on exit. | ||
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=== install.packages() === <!--T:69--> | === install.packages() === <!--T:69--> | ||
To install packages from [https://cran.r-project.org/ CRAN], you can use < | To install packages from [https://cran.r-project.org/ CRAN], you can use <code>install.packages</code> while running an interactive R session on the cluster's login node. Many R packages are developed using the GNU family of compilers so we recommend that you load a <code>gcc</code> [[Utiliser des modules/en|module]] before trying to install any R packages. Use the same version of the <code>gcc</code> for all packages you install. | ||
{{Command | {{Command | ||
|module load gcc/9.3.0 r/4.0.2 | |module load gcc/9.3.0 r/4.0.2 | ||
}} | }} | ||
==== Installing for a specific R version ==== <!--T:18--> | ==== Installing for a specific R version ==== <!--T:18--> | ||
For example, to install the < | For example, to install the <code>sp</code> package that provides classes and methods for spatial data, use the following command on a login node: | ||
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If the argument < | If the argument <code>repos</code> is not specified, you will be asked to select an appropriate mirror for download. Ideally, it will be geographically close to the cluster you're working on. | ||
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Some packages require defining the environment variable < | Some packages require defining the environment variable <code>TMPDIR</code> before installing. | ||
==== Installing for one or many R versions ==== <!--T:79--> | ==== Installing for one or many R versions ==== <!--T:79--> | ||
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In your submission script, you then have to load the desired R module and set the local library directory with < | In your submission script, you then have to load the desired R module and set the local library directory with <code>export R_LIBS=~/.local/R/$EBVERSIONR/</code>. | ||
=== Dependencies === <!--T:5--> | === Dependencies === <!--T:5--> | ||
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=== Downloaded packages === <!--T:22--> | === Downloaded packages === <!--T:22--> | ||
To install a package that you downloaded (i.e. not using <code>install.packages()</code>), you can install it as follows. Assuming the package is named < | To install a package that you downloaded (i.e. not using <code>install.packages()</code>), you can install it as follows. Assuming the package is named <code>archive_package.tgz</code>, run the following command in a shell: | ||
{{Command | {{Command | ||
|R CMD INSTALL -l 'path for your local (home) R library' archive_package.tgz | |R CMD INSTALL -l 'path for your local (home) R library' archive_package.tgz | ||
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Using the R command < | Using the R command <code>system()</code> you can execute commands in the ambient environment from inside R. On our clusters, this can lead to problems because R will give an incorrect value to the environment variable <code>LD_LIBRARY_PATH</code>. You can avoid this problem by using the syntax <code>system("LD_LIBRARY_PATH=$RSNT_LD_LIBRARY_PATH <my system call>")</code> in your R system calls. | ||