cc_staff
311
edits
R: Difference between revisions
Jump to navigation
Jump to search
Marked this version for translation
(Added installation to local library directory) |
(Marked this version for translation) |
||
| Line 91: | Line 91: | ||
=== install.packages() === <!--T:69--> | === install.packages() === <!--T:69--> | ||
To install packages from [https://cran.r-project.org/ CRAN], you can use <tt>install.packages</tt> 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 <tt>gcc</tt> [[Utiliser des modules/en|module]] before trying to install any R packages. Use the same version of the <tt>gcc</tt> for all packages you install. | To install packages from [https://cran.r-project.org/ CRAN], you can use <tt>install.packages</tt> 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 <tt>gcc</tt> [[Utiliser des modules/en|module]] before trying to install any R packages. Use the same version of the <tt>gcc</tt> for all packages you install. | ||
{{Command | {{Command | ||
|module load gcc/7.3.0 r/4.0.2 | |module load gcc/7.3.0 r/4.0.2 | ||
}} | }} | ||
==== Installing for a specific R version ==== | ==== Installing for a specific R version ==== <!--T:18--> | ||
For example, to install the <tt>sp</tt> package that provides classes and methods for spatial data, use the following command on a login node: | For example, to install the <tt>sp</tt> package that provides classes and methods for spatial data, use the following command on a login node: | ||
| Line 113: | Line 112: | ||
Some packages require defining the environment variable <tt>TMPDIR</tt> before installing. | Some packages require defining the environment variable <tt>TMPDIR</tt> before installing. | ||
==== Installing for one or many R versions ==== | ==== Installing for one or many R versions ==== <!--T:79--> | ||
Specify the local installation directory according to currently R module that is loaded. | Specify the local installation directory according to currently R module that is loaded. | ||
{{Commands | {{Commands | ||
| Line 122: | Line 121: | ||
{{Command|R -e 'install.packages("sp", repos{{=}}"https://cloud.r-project.org/")'}} | {{Command|R -e 'install.packages("sp", repos{{=}}"https://cloud.r-project.org/")'}} | ||
<!--T:80--> | |||
In your submission script, you then have to load the desired R module and set the local library directory with <tt>export R_LIBS=~/.local/R/$EBVERSIONR/</tt>. | In your submission script, you then have to load the desired R module and set the local library directory with <tt>export R_LIBS=~/.local/R/$EBVERSIONR/</tt>. | ||