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For the installation of R-packages by users with the help of rstudio or Rscript, the appropriate compiler module must be loaded in addition to the R-module.
R at HLRN
Modules
Befor starting R, load a modulefile
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This provides access to the script R that sets up an environment and starts the R-binary. The corresponding man - and info pages become available.
Info pages: R-admin, R-data, R-exts, R-intro, R-lang, R-admin, R-FAQ, R-ints
As programming environment, rstudio Version 1.1.453 is installed and available, when a module file for R is loaded. rstudio starts the version of R specified with the module file.
Running R on the frontends
This is possible, but the ressources and runtime are is limited. Be friendly to other users and work on the shared compute nodes!
Running R on the compute nodes
Allocate capacity in the batch system, and log onto the related node:
$ salloc -N 1 -p largelarge96:shared $ squeue --job <jobID>
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Load a module file and work interactively as usual. When ready, free the ressources:
$ scancel <jobID>
R packages
List of installed R packages
The following packages are addedby default, when a new version of R is installed. Please contact support to extend this list.
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Users may request package installation via support or install in their HOME - directory.
Building R-packages
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from rstudio or Rscript - users approach
R users may install their own packages in the HOME-directory. R-packages must be build with the same compiler as R itself was build, see the table above. This happens, when Rscript is used and the appropriate compiler module is loaded. R users may install their own packages in the HOME-directory.
Building R-packages - administrators approach
R administrators may use rstudio or Rscript directly. Hence, for installing packages in /sw it is required, to use Rscript like
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Using INSTALL_opts="--html" keeps documentation of installed packages up to date!
This is not appropriate, when installing a huge bundle of packages. For convinience, there is a list of default packages, scripts to install them are available in the installation directory:
- install_packages,
- install_cran
- install_package, github
- install_bioc
- remove_package,
- sync_phywiki
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- wiki
Here also the workarounds are collected needed to install stiff packages.
Other users may request package installation via support or install in their HOME - directory.
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