Package Installation
You can customize the location of user packages installed from CRAN as well as the default CRAN repository. You can also configure the user-interface of RStudio Pro to discourage end-user package installation in the case where packages are deployed centrally to a site library.
The settings discussed in this section are specified in the /etc/rstudio/rsession.conf file (rather than the rserver.conf file previously referenced).
User library
By default R packages are installed into a user-specific library based on the contents of the R_LIBS_USER environment variable (more details on this mechanism are here: http://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html).
It’s also possible to configure an alternative default for user package installation using the r-libs-user setting. For example:
/etc/rstudio/rsession.conf
r-libs-user=~/R/library/%vR interprets %v to be the major.minor version of R; for example the above would cause R 4.2 to use a package library located at ~/R/library/4.2.
Unversioned R library
R doesn’t guarantee ABI compatibility between minor versions, so when you use packages that include compiled code, you will want to ensure that each version of R has its own library. Otherwise, compiled code may cause crashes or other unexpected behavior when R is upgraded.
However, if you do not use any compiled packages, you can share a library between R versions (e.g. just ~/R/library). This makes it possible to upgrade the major version of R on the server and have user’s packages continue to work.
Upgrading R
You can read more about package library considerations when upgrading R in the following article: Upgrading to a New Version of R
Discouraging user installations
It may be that you’ve configured Posit Workbench with a site package library that is shared by all users. In this case you might wish to discourage users from installing their own packages by removing the package installation UI from the RStudio Pro. To do this you use the allow-package-installation setting. For example:
/etc/rstudio/rsession.conf
allow-package-installation=0Note that this setting merely discourages package installation by removing user-interface elements. It’s still possible for users to install packages directly using the utils::install.packages function.
CRAN repositories
By default, RStudio Pro sessions use Posit Public Package Manager’s CRAN repository. Package Manager delivers Posit-built binary CRAN packages. Binary packages are recommended when available for your Linux distribution, as they are faster to install than source packages and don’t require most additional build dependencies. Visit Posit Public Package Mananger for more information.
However, you can override the default CRAN repository. Configure this with the r-cran-repos settings. For example:
/etc/rstudio/rsession.conf
r-cran-repos=http://cran.at.r-project.org/Whatever the default CRAN mirror is, individual users are still able to set their own default. To discourage this, you can set the allow-r-cran-repos-edit settings. For example:
/etc/rstudio/rsession.conf
allow-r-cran-repos-edit=0Note that even with user editing turned off it’s still possible for users to install packages from alternative repositories by directly specifying the repos parameter in a call to install.packages.
To specify a list of CRAN repos, define a /etc/rstudio/repos.conf file containing the primary CRAN repo and named secondary repos. For example:
/etc/rstudio/repos.conf
CRAN=https://packagemanager.posit.co/cran/__linux__/rhel9/latest
Australia=https://cran.ms.unimelb.edu.au/
Austria=https://lib.ugent.be/CRAN/To change the location of repos.conf, use the r-cran-repos-file setting. For example, by adding to rsession.conf:
r-cran-repos-file=/etc/rstudio/mirrors.confOptionally, enable CRAN repos for users in RStudio Pro with the r-cran-repos-url setting. This setting expects a URL to retrieve a configuration file containing the named secondary repositories. These secondary repositories won’t be set by default, but rather, RStudio Pro lists them for users to be manually added to their repository selection. For example:
http://custom-domain/repos.conf
Australia=https://cran.ms.unimelb.edu.au/
Austria=https://lib.ugent.be/CRAN/Notice that the allow-r-cran-repos-edit option can also be used to disallow secondary repos and that repos.conf overrides the r-cran-repos setting, if specified.
For more information on configuring CRAN repository defaults, see Setting Default Repositories in Workbench.
Installations and upgrades automated by RStudio Pro IDE
Several key features of the RStudio Pro IDE (shiny apps, markdown documents, version control, etc.) depend on specific versions of various R packages, and these versions typically increase with each release. By default, the RStudio Pro IDE checks if those packages are installed. If not, it will attempt to install them.
In cases where an upgrade to the latest required version of those packages is not possible (e.g. when running an old R version), the package version check can be disabled by setting
RSTUDIO_DISABLE_PACKAGE_INSTALL_PROMPT=yesin rsession-profile.
Please note: Enabling this feature will disable both the check for package version and package availability on your system. If required packages are missing, some features of the IDE may not work. Use at your own risk.