bspm: Bridge to System Package Manager

Enables binary package installations on Linux distributions. Provides functions to manage packages via the distribution’s package manager. Also provides transparent integration with R’s install.packages() and a fallback mechanism. When installed as a system package, interacts with the system’s package manager without requiring administrative privileges via an integrated D-Bus service; otherwise, uses sudo. Currently, the following backends are supported: DNF, APT.

Installation

Installation from system repositories is preferred, mainly to avoid issues on SELinux-enabled systems (see #19).

• For Fedora, see R-CoprManager for the cran2copr project.
• For Ubuntu/Debian, it is available as r-cran-bspm via APT.

Installation from source requires the following dependencies (apart from R):

• python3-dnf (Fedora-like), python3-apt (Debian-like)

If you plan to run it as a regular user (non-root), these are required too:

• systemd
• python3-dbus
• python3-gobject (Fedora-like), python3-gi (Debian-like)

Then, you should install it as a system package to be able to use it as a regular user (note sudo):

sudo R CMD INSTALL bspm_[version].tar.gz

Further configuration options:

• If you plan to run it only as root (e.g., in a docker container), then you don’t need the D-Bus service, so you can disable its installation by adding --configure-args="--without-dbus-service".
• If you are installing the package in a build root, instead of its final destination, specify --configure-vars="BUILD_ROOT=[path_to_build_root]" too.
• By default, package prefixes and exclusions are automatically discovered from system repositories, and this discovery mechanism is exposed so that the user can install other packages if e.g. new repositories with other prefixes are added. If you want to fix prefixes and exclusions and prevent exposing the discovery mechanism, set --configure-vars="PKG_PREF='prefix1- prefix2- ...'" and --configure-vars="PKG_EXCL='exclusion1 exclusion2 ...'".

To enable it by default, put the following into the Rprofile.site:

suppressMessages(bspm::enable())

Then, run install.packages as usual, and available system packages will be automatically installed.

Developing new backends

New backends for other package managers can be added to inst/service/backend. Each backend must implement the following functions:

• def discover() -> dict({ "prefixes" : list, "exclusions" : list })
• def install(prefixes : list, pkgs : list, exclusions : list) -> list
• def remove(prefixes : list, pkgs : list, exclusions : list) -> list

The last two functions receive a list of prefixes, a list of R package names and a list of exclusions, and must return a list with those package names that could not be processed (i.e., packages not found in the system repos). Any progress should be reported to stdout.