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bspm: Bridge to System Package Manager

Build Status Coverage Status CRAN_Status_Badge Downloads

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, ALPM.

See our contributed talk at useR! 2021: [video, slides].

Installation

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

  • Follow these links if the target system is a desktop/server installation of one of the supported distributions: Fedora, Ubuntu, openSUSE, Arch.
  • If the target system is a containerized application (e.g., a Docker image), refer to the rocker/r-bspm images.
  • If you are trying bspm in another distro, or you are packaging it as a system package, please follow the general procedure below.

General procedure

Installation from source requires (apart from R) the folllowing Python bindings:

Package manager DBus (*) GObject (*)
Fedora/RedHat python3-dnf python3-dbus python3-gobject
Ubuntu/Debian python3-apt python3-dbus python3-gi
openSUSE python3-dnf python38-dbus-python python3-gobject
Arch pyalpm python-dbus python-gobject

(*) Optional, only required if you plan to run bspm as a regular user (non-root) in a (systemd-based) desktop/server setting.

Then, you should install bspm as a system package to be able to use it as a regular user. Download the latest version from CRAN or GitHub and proceed with the installation (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:

> bspm::enable() # wrap it in suppressMessages() to avoid the initial message

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

Fedora

There are thousands of binary packages available via the iucar/cran Copr repo. The bspm package is available as R-CoprManager, and enabled by default:

$ dnf --version | grep -q dnf5 || sudo dnf install 'dnf-command(copr)'
$ sudo dnf copr enable iucar/cran
$ sudo dnf install R-CoprManager

Ubuntu

(Essentially) all of CRAN is available as binary packages via the r2u repo:

$ . /etc/os-release # to get UBUNTU_CODENAME
$ URL="https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts"
$ curl -s "${URL}/add_cranapt_${UBUNTU_CODENAME}.sh" | sudo bash -s

openSUSE

There are thousands of binary packages available via the autoCRAN OBS repo:

$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_Tumbleweed/devel:languages:R:patched.repo
$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
$ sudo zypper install R-patched python3-dnf python38-dbus-python python3-gobject
$ sudo ln -s /etc/zypp/repos.d /etc/yum.repos.d

Then, install bspm as a system package from CRAN:

$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'

Then, to enable it system-wide (alternatively, use your .Rprofile):

$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site

Sometimes, a restart is required so that the new systemd service is recognized.

Arch

There are thousands of binary CRAN and Bioconductor packages available via the BioArchLinux repo:

$ echo -e "\n[bioarchlinux]\nServer = https://repo.bioarchlinux.org/\$arch" \
  | sudo tee -a /etc/pacman.conf
$ sudo pacman-key --recv-keys B1F96021DB62254D
$ sudo pacman-key --lsign-key B1F96021DB62254D
$ sudo pacman -Syu r-bspm

Then, to enable it system-wide (alternatively, use your .Rprofile):

$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site

Moving the user library

After installing and enabling bspm in a system with a populated user library, package shadowing will prevent system packages from loading, because the user library takes precedence in .libPaths() (see ?bspm::shadowed_packages for an utility to find shadowed packages). To solve this, it is necessary to install packages available in the system repos and remove them from the user library, leaving there only GitHub packages, development versions, and so on. This is achieved simply by calling bspm::moveto_sys().

Additionally, bspm provides a script for mass-calling bspm::moveto_sys() for several users and/or libraries, which allows sysadmins to easily deploy bspm in a multi-user server. The script, which requires sudo privileges, is called as follows:

$ Rscript -e bspm:::scripts mass_move user1 [user2 ...] [lib1 [lib2 ...]]

By default, it does a dry run, meaning that it won't touch anything and will just report the user libraries found. To actually run the script, the --run flag must be provided:

$ Rscript -e bspm:::scripts mass_move --run user1 [user2 ...] [lib1 [lib2 ...]]

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 available(prefixes : list, exclusions : list) -> 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.

Support and troubleshooting

If you are experiencing an issue that is not listed here, or the solution did not work for you, please do not hesitate to open a ticket at our GitHub issue tracker.

Cannot connect to the system package manager

Symptom: you tried to install a package and you got this message.

> install.packages(<some_package>)
Error in install.packages : cannot connect to the system package manager

This usually happens when bspm was installed in the user library or, as a system package, it is not properly configured for some reason. The solution is:

  1. First and foremost, uninstall any copy of bspm in your user library.
  2. Reinstall with admin privileges, e.g.:
$ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")'