Manage Packages from System Repositories

Talk to the system package manager to install/remove... packages from system repositories (see details for further options).

Usage

install_sys(pkgs)

remove_sys(pkgs)

moveto_sys(lib, newer = FALSE)

available_sys()

discover()

Arguments

pkgs: character vector of names of packages.
lib: a character vector giving the library directories to remove the packages from. If missing, defaults to the first element in R_LIBS_USER.
newer: whether to move newer packages from the user library. The special value "ask" is also supported.

Value

Functions install_sys, remove_sys, and moveto_sys

return, invisibly, a character vector of the names of packages not available in the system.

Function available_sys returns a matrix with one row per package. Row names are the package names, and column names include "Package", "Version", "Repository".

Details

If R runs with root privileges (e.g., in a docker container), these functions talk directly to the system package manager. Regular users are also able to install/remove packages without any administrative permission via the accompanying D-Bus service if bspm is installed as a system package. If not, these methods fall back on using sudo to elevate permissions (or pkexec in GUIs such as RStudio) in interactive sessions. Note that, if you want to fall back to sudo in a non-interactive session, you need to set options(bspm.sudo=TRUE).

If options(bspm.sudo.autodetect=TRUE), bspm tries to detect whether it is running in an environment where password-less sudo can be used (e.g., in a containerized environment such as a Fedora Toolbox) for every call, and then uses sudo accordingly.

The moveto_sys method moves existing user packages to the system library to avoid package shadowing (i.e., installs the available system packages and removes copies from the user library; see shadowed_packages). This provides a mechanism to easily deploy bspm on an existing R installation with a populated user library.

The discover method is only needed when e.g. a new repository is added that contains packages with different prefixes (for example, your system repositories may provide packages called r-cran-* and r-bioc-* and then you add a new repository that provides packages called r-github-*). Otherwise, it will not have any effect besides regenerating the internal configuration files.

Examples

if (FALSE) {
# install 'units' and all its dependencies from the system repos
bspm::install_sys("units")

# now remove it
bspm::remove_sys("units")

# get available packages
bspm::available_sys()
}