| Title: | Bridge to System Package Manager |
|---|---|
| Description: | 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. |
| Authors: | Iñaki Ucar [aut, cph, cre] |
| Maintainer: | Iñaki Ucar <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.5.7.2 |
| Built: | 2024-11-07 05:58:13 UTC |
| Source: | https://github.com/cran4linux/bspm |
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.
Iñaki Ucar
https://cran4linux.github.io/bspm/
manager, integration,
bspm-scripts, bspm-options
List of options() supported to configure bspm's behavior.
In general, these should be set before calling any package function.
bspm.backend.check:logical, default TRUE. If false,
the initial check on enable() is not performed.
bspm.version.check:logical, default TRUE. If false,
as many binaries are installed as possible without any version check,
and then installation from source is used as a fallback.
bspm.sudo.autodetect:logical, default FALSE. If true,
enables autodetection and selection of password-less sudo.
bspm.sudo:logical, default FALSE. If true, forces
sudo unconditionally as the preferred mechanism.
These are used in the same way as in base R. See options for
a detailed description.
askYesNo
install.packages.compile.from.source
Internal scripts can be called via Rscript (see examples).
## Not run: # get a list of available scripts with descriptions Rscript -e bspm:::scripts # see a script's help Rscript -e bspm:::scripts <script_name> -h # run a script Rscript -e bspm:::scripts <script_name> [args] ## End(Not run)## Not run: # get a list of available scripts with descriptions Rscript -e bspm:::scripts # see a script's help Rscript -e bspm:::scripts <script_name> -h # run a script Rscript -e bspm:::scripts <script_name> [args] ## End(Not run)
Functions to enable or disable the integration of install_sys
into install.packages. When enabled, packages are installed
transparently from system repositories if available, including dependencies,
and from the configured R repositories if not.
enable() disable()enable() disable()
To enable bspm system-wide by default, include the following:
suppressMessages(bspm::enable())
into the Rprofile.site file. To enable it just for a particular user,
move that line to the user's ~/.Rprofile instead.
By default, enabling bspm triggers a check of the backend, and a
warning is raised if the system service is required but not available. To
avoid this check, options(bspm.backend.check=FALSE) can be set.
Enabling bspm sets default installation type to "both",
which means 'use binary if available and current, otherwise try source'.
The action if there are source packages which are preferred is controlled by
getOption("install.packages.compile.from.source"). Set this option to
"never" to always prefer binaries over source packages, with an
informative message about newer versions available from source.
If binaries are always preferred and no message is required, a special
fast mode can be enabled via options(bspm.version.check=FALSE),
(true by default) which completely skips version checking.
## Not run: # install 'units' and all its dependencies from the system repos bspm::enable() install.packages("units") # install packages again from CRAN bspm::disable() install.packages("errors") ## End(Not run)## Not run: # install 'units' and all its dependencies from the system repos bspm::enable() install.packages("units") # install packages again from CRAN bspm::disable() install.packages("errors") ## End(Not run)
Talk to the system package manager to install/remove... packages from system repositories (see details for further options).
install_sys(pkgs) remove_sys(pkgs) moveto_sys(lib, newer = FALSE) available_sys() discover()install_sys(pkgs) remove_sys(pkgs) moveto_sys(lib, newer = FALSE) available_sys() discover()
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 |
newer |
whether to move newer packages from the user library.
The special value |
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.
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".
## Not run: # 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() ## End(Not run)## Not run: # 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() ## End(Not run)
Find packages that are shadowed by others in library locations with a higher priority.
shadowed_packages(lib.loc = NULL)shadowed_packages(lib.loc = NULL)
lib.loc |
character vector describing the location of the R library
trees to search through, or |
R supports setting several locations for library trees. This is a
powerful feature, but many times packages end up installed in multiple
locations, and in such cases R silently uses the one in the path with the
highest priority (appearing first in .libPaths), thus
shadowing packages in locations with a lower priority.
For bspm installations, this means that outdated user packages may
break system libraries. This utility reports packages that are shadowed
(one per row) with information on which location ("Shadow.LibPath")
and version ("Shadow.Version") has priority over it.
The moveto_sys method is a great complement to move such
outdated versions to the system libraries.
A data.frame with one row per package, row names the package
names and column names (currently) "Package", "LibPath", "Version",
"Shadow.LibPath", "Shadow.Version", "Shadow.Newer".