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 from system repositories is preferred, mainly to avoid issues on SELinux-enabled systems (see #19).
rocker/r-bspm images.bspm in another distro, or you are packaging it as a system package, please follow the general procedure below.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):
Further configuration options:
--configure-args="--without-dbus-service".--configure-vars="BUILD_ROOT=[path_to_build_root]" too.--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:
Then, run install.packages as usual, and available system packages will be automatically installed.
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:
$ sudo dnf install 'dnf-command(copr)'
$ sudo dnf copr enable iucar/cran
$ sudo dnf install R-CoprManagerThere are thousands of binary packages available via the c2d4u.team/c2d4u4.0+ PPA repo:
$ sudo add-apt-repository ppa:marutter/rrutter4.0 # R v4.0 and higher
$ sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ # R packages
$ sudo apt-get update && sudo apt-get install python3-{dbus,gi,apt}Then, install bspm as a system package from CRAN:
Then, to enable it system-wide (alternatively, use your .Rprofile):
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.dThen, install bspm as a system package from CRAN:
Then, to enable it system-wide (alternatively, use your .Rprofile):
Sometimes, a restart is required so that the new systemd service is recognized.
There are a number of binary CRAN packages available via the ArchRPkgs repo as well as Bioconductor packages via the BioArchLinux repo:
$ echo -e "\n[desolve]\nServer = https://desolve.ru/archrepo/\$arch" \
"\n[bioarchlinux]\nServer = https://repo.bioarchlinux.org/\$arch" \
| sudo tee -a /etc/pacman.conf
$ sudo pacman -Sy && sudo pacman -S r pyalpm python-{dbus,gobject}Then, install bspm as a system package from CRAN:
Then, to enable it system-wide (alternatively, use your .Rprofile):
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:
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:
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) -> listdef install(prefixes : list, pkgs : list, exclusions : list) -> listdef remove(prefixes : list, pkgs : list, exclusions : list) -> listThe 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.
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.
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 managerThis 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:
bspm in your user library.